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hgu95av2cdf License: Artistic-2.0 MD5sum: db90cdcf13bc3da0eefbdf14ef1129a9 Package: affycoretools Version: 1.84.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 MD5sum: 87b6dfc28b957b5846040bb79800d87b Package: affyILM Version: 1.64.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 MD5sum: b37d148e0f615da8d612500d93de02c4 Package: affyio Version: 1.82.0 Depends: R (>= 2.6.0) Imports: methods License: LGPL (>= 2) MD5sum: 1792c49bd1052a4d3a5a66bfe10ce543 Package: affylmGUI Version: 1.86.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi, 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BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) License: MIT + file LICENSE MD5sum: d4c9230e06a84a2845ccdaa7bbb31e06 Package: altcdfenvs Version: 2.74.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: 591abdc5cf79b48a6944a4f50e9f781f Package: AMARETTO Version: 1.28.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: 95c1c92dd7b8074dedb21fd6920604be Package: AMOUNTAIN Version: 1.38.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: d8a85d7f761caed0e6c07e307857cfb9 Package: amplican Version: 1.34.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.61.1), Seqinfo, BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), data.table (>= 1.10.4-3), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4), rlang (>= 1.2.0) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: 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SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 4aa3858161e6ad83a350a0196945758a Package: ANF Version: 1.34.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6b606077a7cf7ff39aedf06e15c92749 Package: anglemania Version: 1.2.0 Depends: R (>= 4.5.0) Imports: bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix, pbapply, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, withr LinkingTo: Rcpp, rmio, bigstatsr Suggests: batchelor, BiocStyle, bluster, knitr, magick, matrixStats, patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat, splatter, testthat (>= 3.0.0), UpSetR License: GPL (>= 3) MD5sum: 48e2c5605cf39b7f6aca5081ca3278ae Package: animalcules Version: 1.28.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 718fda2597d5637a4eb048c7d592e730 Package: annaffy Version: 1.84.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: b496f1d87d18827fefdb4d2f880ea287 Package: anndataR Version: 1.2.1 Depends: R (>= 4.5.0) Imports: cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0), reticulate (>= 1.41.1), rlang, stats Suggests: BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1), Rarr (>= 1.11.12), rmarkdown, S4Vectors, Seurat, SeuratObject, SingleCellExperiment, spelling, SummarizedExperiment, testthat (>= 3.0.0), vctrs, withr, yaml License: MIT + file LICENSE MD5sum: 14f3e7aef7afba444a75f9a660540392 Package: annmap Version: 1.54.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 80c9d449bcb733f86f363c40e6528b0e Package: annoLinker Version: 1.0.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocGenerics, future.apply, GenomicRanges, GenomeInfoDb, igraph, IRanges, InteractionSet, methods, progressr, S4Vectors, Seqinfo, trackViewer, visNetwork Suggests: BiocStyle, knitr, rtracklayer, rmarkdown, testthat, TxDb.Drerio.UCSC.danRer10.refGene, org.Dr.eg.db, future License: GPL-3 MD5sum: 732b08e15f831b9a1a940d37590d73fd Package: annotate Version: 1.90.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1757cd2255b79b77f98692113934df13 Package: AnnotationDbi Version: 1.74.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 37e130e569ff74351ab431f8ed8258b1 Package: AnnotationFilter Version: 1.36.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: da5854d5fcfe8e0332178d65888b5201 Package: AnnotationForge Version: 1.54.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: 1282ae4968714257e317808d64540f20 Package: AnnotationHub Version: 4.2.2 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2, yaml, dplyr, BiocBaseUtils Suggests: IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 68880b552c14318e1000c7845cd1296e Package: AnnotationHubData Version: 1.42.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, Seqinfo, GenomeInfoDb (>= 1.45.5), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 088519eece780d1edad87a4673d0f165 Package: annotationTools Version: 1.86.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 8653f529667281458f0589faba5d880a Package: annotatr Version: 1.38.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2 (>= 3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang, rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils Suggests: GenomeInfoDb, BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Drerio.UCSC.danRer11.refGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene License: GPL-3 MD5sum: 49c547267841a974868be32238fd67b1 Package: anota Version: 1.60.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: d66ffdeb51b23f2bc2908479d30fad86 Package: anota2seq Version: 1.34.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: 07a04627bdff98518ce4438059334c7f Package: antiProfiles Version: 1.52.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 6563dbaed27107b24183d50ebd52ce52 Package: AnVIL Version: 1.24.1 Depends: R (>= 4.5.0), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, GCPtools, jsonlite, httr, digest, keyring, rapiclient, yaml, tibble, shiny, DT, miniUI, htmltools, BiocBaseUtils Suggests: knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: 647be42805e98338865d09f5ca0c8dc4 Package: AnVILAz Version: 1.6.0 Depends: R (>= 4.5.0) Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 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rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, GCPtools, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7470062035f14ed85e4480721a9e3cc8 Package: APAlyzer Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, rlang, txdbmaker, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset, HybridMTest License: LGPL-3 + file LICENSE MD5sum: d95ed3f537f26fefb136599f8d463010 Package: apComplex Version: 2.78.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: d48abc2415ea328f5e705496759eb917 Package: apeglm Version: 1.34.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 423c6dc7d99ad9847b9ccb89f61d9dbb Package: APL Version: 1.16.0 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: 2e8e4f4c77e1bf0d5ef0a172e9cd2ddd Package: appreci8R Version: 1.30.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, 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stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 037f825f5559d09f897277b64da2fda2 Package: ASAFE Version: 1.38.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 6b02a2f627900c01caaf71821656e26d Package: ASEB Version: 1.56.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 89c59d73c3dd7160572df9bee63ca622 Package: ASGSCA Version: 1.46.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 449d0adfc831d1f3d3a686a3b5d810df Package: ASICS Version: 2.28.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: c589a43f48480b12c2708345d44c54d1 Package: ASpli Version: 2.22.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: 240762939e87e48c9a3cbe3c216f0b44 Package: AssessORF Version: 1.30.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: cf7d6f8901b154729e69e9ba0b493aab Package: ASSET Version: 2.30.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 2ff0c90c27b10fdfd1b6f9afadaa5e74 Package: ASSIGN Version: 1.48.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8d552bbc9b5748fadbd1abfa3ade49c2 Package: assorthead Version: 1.6.3 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 0f3d321df3b54cc0ac2c33b6fc0c1572 Package: ASURAT Version: 1.16.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 5465cac51de0d4e480a4fdbd69fbcf21 Package: asuri Version: 1.0.0 Depends: R (>= 4.5.0), stats, methods Imports: SummarizedExperiment, spsUtil, lubridate, survival, glmnet, siggenes, survcomp, scales, ROCR, ggplot2, grDevices, graphics, utils, Rdpack Suggests: BiocStyle, knitr, formatR, rmarkdown, magick, devtools License: LGPL-3 + file LICENSE MD5sum: 3e5da73246cc74e23e28019066bed40b Package: atacInferCnv Version: 1.0.0 Depends: R (>= 4.5.0),utils Imports: infercnv (>= 1.3.1), Signac, Seurat, GenomicRanges, GenomeInfoDb, S4Vectors, config, stringr, ggplot2, SummarizedExperiment, SingleCellExperiment, Rcpp LinkingTo: Rcpp,RcppEigen Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 0a44a17ee032a85c436a6a122102739c Package: ATACseqQC Version: 1.36.1 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, polynom, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 7faa5d57233324acf2c426bf2c6fb9c9 Package: ATACseqTFEA Version: 1.14.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: e6f6b484c12220368967c84b94ea8fce Package: atena Version: 1.18.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: c986230abc30aeef1f35e438e32b3b06 Package: atSNP Version: 1.28.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: b3adef9aa46d3934c96597aaf9cbecf6 Package: attract Version: 1.64.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: f5feab9cf923343a960bf7c3aedeec06 Package: AUCell Version: 1.34.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: a49d572d189926f535bc59f545c582db Package: autonomics Version: 1.20.0 Depends: R (>= 4.0) Imports: abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, lme4, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, survival, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite, knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: d290f125e04197c8ab1feb09a84e1c24 Package: AWAggregator Version: 1.2.0 Depends: R (>= 4.5.0) Imports: dplyr, Peptides, progress, purrr, ranger, rlang, stats, stringr, tidyr, toOrdinal, utils Suggests: AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1093351266cea5bdd54497582435bf73 Package: AWFisher Version: 1.26.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 3d722a14bf3aeab6d0c119ca3208a444 Package: awst Version: 1.20.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 848c7ce9adf18c1a77794f5f0c444215 Package: BaalChIP Version: 1.38.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: f768f6f8d6c4738452a3d4f866b6b7b6 Package: bacon Version: 1.40.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: bb029d040e0f87af94377253501f081e Package: BADER Version: 1.50.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: f34cf5907c9b27a8ac58cac6079d80f5 Package: BadRegionFinder Version: 1.40.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 782a99303bc337f5b11fb414f82de525 Package: BAGS Version: 2.51.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 1cb7d693415b59bc549fa61541e52ff1 Package: bambu Version: 3.14.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 41cf014c1158b1386c9b4fa93853589a Package: bamsignals Version: 1.44.1 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: b7325ddca0f0f9869feea5ff82344146 Package: BANDITS Version: 1.28.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 7bd09226db971b6f7785c5563f4eeda4 Package: bandle Version: 1.16.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 5534440be9c15b678cd56b9cd7cde0af Package: Banksy Version: 1.8.1 Depends: R (>= 4.4.0) Imports: aricode, BiocParallel, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian, GenomeInfoDb Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: 691d57c9e02fb651161eca08183f4c58 Package: banocc Version: 1.36.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: b33a389645db66d265d366c5e32a0176 Package: barbieQ Version: 1.4.0 Depends: R (>= 4.5) Imports: magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap, ggplot2, logistf, limma, stats, igraph, utils, data.table, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 5a2f7ad599371c53b92a00a61c45ac7e Package: BaseSpaceR Version: 1.56.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 491a012d546530e7850511aaa07b12ff Package: Basic4Cseq Version: 1.48.0 Depends: R (>= 3.5.0), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: ee38f4e0cdf5e7881d7c49c11cf31f2a Package: BASiCS Version: 2.24.0 Depends: R (>= 4.1), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: cf890ec3a736984a37d72eacb1a8f30b Package: BASiCStan Version: 1.14.1 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: a571ec729cd2da5a66760bde5cedd270 Package: BasicSTARRseq Version: 1.40.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,Seqinfo,stats Suggests: knitr License: LGPL-3 MD5sum: 9fae32642cf101f7dab55a738adb3541 Package: basilisk Version: 1.24.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 4e9bd97ea56f7050a638b4fd3bd26260 Package: basilisk.utils Version: 1.24.0 Imports: utils, methods, tools, dir.expiry Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 45a817a0128be3713f8a5100aca5c7e1 Package: batchCorr Version: 1.2.0 Depends: R (>= 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DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: 7470091aa5eb815a503ffeb57718ba7f Package: BatchQC Version: 2.8.1 Depends: R (>= 4.5.0) Imports: data.table, DESeq2, dplyr, EBSeq, edgeR, FNN, ggdendro, ggnewscale, ggplot2, ggpubr, Harman, limma, matrixStats, methods, MASS, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse, umap, utils Suggests: BiocManager, BiocStyle, bladderbatch, curatedTBData, devtools, knitr, lintr, MultiAssayExperiment, plotly, rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ae736837a98cbf851e54afa7b5dce437 Package: BatchSVG Version: 1.4.0 Depends: R (>= 4.5.0) Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment Suggests: testthat (>= 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BiocFileCache, BiocSingular, BiocParallel LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: b5b17d2dea917474de1c5910681ef9fe Package: bayNorm Version: 1.30.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 41ae5cfe5516be9568eed2e1b4289c56 Package: baySeq Version: 2.46.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: c72fb154a0458cab975ae3bbd5d81e84 Package: BBCAnalyzer Version: 1.42.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: c61f0c615b2fe88ad5bcfc959929f52b Package: BCRANK Version: 1.74.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: e9973f993b599267b73139e83b4a6a4e Package: bcSeq Version: 1.33.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 8cdddc08f30b1775c2a797329615e374 Package: beachmat Version: 2.28.0 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead (>= 1.5.4) Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 3ca633098f26ddbc1ce0f98b1692daae Package: beachmat.hdf5 Version: 1.10.0 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: d8331f022d759116f05bd95ed33699ac Package: beachmat.tiledb Version: 1.4.0 Imports: methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix License: GPL-3 MD5sum: 3688bc2205355a6f70a8ebcff42972e0 Package: beadarray Version: 2.62.1 Depends: R (>= 3.5.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, methods, ggplot2, BeadDataPackR Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, knitr License: MIT + file LICENSE MD5sum: a07fe6cab3fdc842ec9ce69cbc749884 Package: BeadDataPackR Version: 1.64.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 05367ada509f5320d4ba8cfc751f2a46 Package: BEAT Version: 1.50.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 86e66857b5b4f64b07118eaa1cf84e81 Package: BEclear Version: 2.28.0 Depends: BiocParallel (>= 1.14.2) Imports: logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: ff489dfd0ce505efbe8b3dfad4c464ce Package: bedbaser Version: 1.4.0 Depends: R (>= 4.5.0) Imports: AnVIL (>= 1.16.0), BiocFileCache, curl, dplyr, GenomeInfoDb, GenomicRanges, httr, methods, purrr, rtracklayer, rlang, R.utils, stats, stringr, tibble, tidyr, tools, utils Suggests: BiocStyle, knitr, liftOver, testthat (>= 3.0.0), withr License: Artistic License 2.0 MD5sum: 735391efb6b1182ac97b9023f4dcaee3 Package: beer Version: 1.15.1 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 282ac5506c0f8f11d26460c90410afa9 Package: benchdamic Version: 1.18.0 Depends: R (>= 4.3.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST, Seurat, ANCOMBC, microbiome, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, maaslin3, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat License: Artistic-2.0 MD5sum: 1d2cae3f5a856bedc695bcea343937ab Package: BERT Version: 1.8.0 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 40eb6a034772433d7f000dece72decfc Package: betaHMM Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 82b81b32bc982a507c425abdeaed63a8 Package: betterChromVAR Version: 1.0.3 Depends: SummarizedExperiment Imports: BiocParallel, Biostrings, GenomicRanges, IRanges, Matrix, matrixStats, methods, S4Vectors, stats Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat License: GPL (>= 3) MD5sum: d18ba162e3caa6dd4752b13311798d3f Package: bettr Version: 1.8.0 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors, jsonlite, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 50f2f4598d27f7aa6e77e07403e2e344 Package: BG2 Version: 1.12.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 15ab1fa87988dbfc0d5ef0e29ac62731 Package: BgeeCall Version: 1.28.4 Depends: R (>= 3.6) Imports: AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar Suggests: knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr License: GPL-3 + file LICENSE MD5sum: c49ba8c77a84d8994e486a37ef65a49e Package: BgeeDB Version: 2.38.1 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: f6d0090295675fa6498746ed4b5ed94a Package: BicARE Version: 1.70.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: 024720addf5a7a5bc64dc32139b52bcd Package: BiFET Version: 1.32.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: 0904b07786562414364b5029f0d63004 Package: bigmelon Version: 1.38.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: 57a9ef7f63d6ea0d66adaac62980e1e3 Package: BindingSiteFinder Version: 2.10.0 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr, txdbmaker, ggrepel, stringr License: Artistic-2.0 MD5sum: a2d966da635e88da320182ff281f8e71 Package: bioassayR Version: 1.50.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: BiocStyle, RCurl, biomaRt, knitr, knitcitations, knitrBootstrap, testthat, 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S4Vectors, Seqinfo, stats, utils, XVector LinkingTo: S4Vectors, XVector, IRanges Suggests: BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData, knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 8fa30d22ee03edf306b9b3b82c58d6e5 Package: bioCancer Version: 1.40.0 Depends: R (>= 4.1.0), radiant.data (>= 0.9.1), cBioPortalData, XML (>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble, GO.db Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: b49f35e4ffc581eeef9cacf180b191cf Package: BioCartaImage Version: 1.10.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, BiocStyle, ragg License: MIT + file LICENSE MD5sum: 716b74aa64326a503dd56184e5a338d9 Package: BiocAzul Version: 1.0.3 Depends: R (>= 4.5.0), AnVIL Imports: AnVILPublish (>= 1.21.1), dplyr, httr, jsonlite, progress, rlang, methods, tidyr Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 0c5c5e2c9aab667c94acb53dfaf9f2c1 Package: BiocBaseUtils Version: 1.14.2 Depends: R (>= 4.5.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 MD5sum: d1894908c293981be10242f7a91d2013 Package: BiocBook Version: 1.10.0 Depends: R (>= 4.3) Imports: BiocGenerics, pak, cli, glue, gert, gh, gitcreds, httr, usethis, dplyr, purrr, tibble, methods, rprojroot, stringr, yaml, tools, utils, rlang, quarto, renv Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 717fdbc296cf04fcedcd469e6dc46d60 Package: BiocBuildReporter Version: 1.0.1 Depends: R (>= 4.5.0) Imports: arrow, 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rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: c6ce378d13d9c88d136407e241076a6d Package: BiocGenerics Version: 0.58.1 Depends: R (>= 4.0.0), methods, utils, graphics, stats, generics Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, S4Arrays, SparseArray, DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, MultiAssayExperiment, RUnit License: Artistic-2.0 MD5sum: 4663ab69a27dfb1e1bf266848ff7f73a Package: biocGraph Version: 1.74.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: a0939b617be5980d4958a81e0ced1e83 Package: BiocHail Version: 1.12.0 Depends: R (>= 4.3.0), graphics, stats, utils Imports: reticulate, basilisk, BiocFileCache, methods, dplyr, BiocGenerics Suggests: knitr, testthat, BiocStyle, ggplot2, DT License: Artistic-2.0 MD5sum: 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rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: f8e53dc6ec62b602ca706bccfdc223f3 Package: bnem Version: 1.20.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: 1263bb0b851b1514df6710f5a5c3918d Package: BOBaFIT Version: 1.16.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: 3212b0f67596f4b78b339382059f8ce3 Package: borealis Version: 1.16.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: cb555fece4556d2c35b1b379258a5ccb Package: BRAIN Version: 1.58.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: fb5993689cd7f70f31089c2f314f0b33 Package: branchpointer Version: 1.38.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, Seqinfo, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 995ec12a5f483471a4fd1ec2d0cf9b6d Package: breakpointR Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 3e36bff674911c05515d4be47b79094d Package: BreastSubtypeR Version: 1.4.0 Depends: R (>= 4.5.0) Imports: methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang, stringr, withr, edgeR, ComplexHeatmap, impute (>= 1.80.0), data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>= 0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8), SummarizedExperiment, utils Suggests: lifecycle, tidyverse, shiny (>= 1.9.1), bslib (>= 0.8.0), BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: cd03fa096fc5f3f0414b712b1fe18a27 Package: brendaDb Version: 1.26.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: 4aa65b05721c3b3dfc2fc6102c5452c0 Package: BREW3R.r Version: 1.8.0 Imports: GenomicRanges, methods, rlang, S4Vectors, utils 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S4Vectors (>= 0.47.6), GenomicRanges (>= 1.61.1), BiocIO, rtracklayer (>= 1.69.1) Suggests: GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 License: Artistic-2.0 MD5sum: f351c63c00e4007ecfb4870a16cf3ecf Package: bsseq Version: 1.48.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), Seqinfo, scales, stats, parallel, tools, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5, beachmat (>= 2.23.2) LinkingTo: Rcpp, beachmat, assorthead (>= 1.1.4) Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, batchtools License: Artistic-2.0 MD5sum: a8f4735245a460adc06647bbf84d4413 Package: 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STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme License: CeCILL | file LICENSE MD5sum: 63a31a0197151c502cc5800ca287a60f Package: BUMHMM Version: 1.36.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 1f2a2d17a6d77508bb919e76ee2f522d Package: bumphunter Version: 1.54.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), Seqinfo, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 5ba14e7025d35d4d13566a97898c8621 Package: BumpyMatrix Version: 1.20.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + 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methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 8be677127015fe0c5d44da962b9098c4 Package: CAGEr Version: 2.18.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, Seqinfo, GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), ggplot2 (>= 4.0.0), gtools, IRanges (>= 2.18.0), KernSmooth, Matrix, memoise, plyr, rlang, Rsamtools (>= 2.25.1), reshape2, rtracklayer (>= 1.69.1), S4Vectors (>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment (>= 1.39.1), utils, vegan, VGAM Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: b06468ff6b46027d3a2aa3934864e164 Package: CalibraCurve Version: 1.2.0 Depends: R (>= 4.5.0) Imports: checkmate, dplyr, ggplot2, magrittr, openxlsx, scales, SummarizedExperiment, tidyr Suggests: BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo, testthat, vdiffr License: BSD 3-clause License + file LICENSE MD5sum: 917292ecdc569270848c924261aa1843 Package: calm Version: 1.26.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: f627d894d28a83b1a2b884f5e89782c0 Package: CAMERA Version: 1.67.0 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics, multtest Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 1623d8642e722ffbca8ffbca49aec8d0 Package: CaMutQC Version: 1.8.0 Depends: R (>= 4.5.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle, shiny License: GPL-3 MD5sum: 96ccef9d3ccbc07d197709f6678f1a6c Package: canceR Version: 1.46.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 10185842fa87dd785f58b11e55545a99 Package: cancerclass Version: 1.56.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 6d0c0164868ab48324a96d01ac0bcb05 Package: cardelino Version: 1.14.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: e1f627b2901f73708490fe498e074d80 Package: Cardinal Version: 3.14.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4, lmerTest License: Artistic-2.0 | file LICENSE MD5sum: d623cc5475fac76a3277115de1471ada Package: CardinalIO Version: 1.10.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: fe63f5d28eb7961d865f752571a279a9 Package: CARDspa Version: 1.4.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.7),RcppArmadillo, SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie, grDevices,ggcorrplot, stats, nnls, BiocParallel, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, RcppML, BiocStyle License: GPL-3 + file LICENSE MD5sum: 2b80f76b6e46af3d70bfdbbd3c39caf3 Package: carnation Version: 1.0.1 Depends: R (>= 4.5.0) Imports: BiocParallel, colorspace, ComplexUpset, dendextend, DESeq2, dplyr, DT, enrichplot, GeneTonic, ggplot2, ggrepel, heatmaply, htmltools, igraph, methods, MatrixGenerics, plotly, reticulate, RColorBrewer, rintrojs, scales, shiny, shinyBS, shinycssloaders, shinymanager, shinythemes, shinyWidgets, sortable, SummarizedExperiment, tools, utils, viridisLite, visNetwork, yaml Suggests: airway, BiocStyle, DEGreport, GenomicFeatures, goseq, knitr, org.Hs.eg.db, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 640fdf7fd55c3561958daf434bcfa6ff Package: CARNIVAL Version: 2.22.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 0a980ce6c1ea768a91439a6f3b3c4bb0 Package: CATALYST Version: 1.36.0 Depends: R (>= 4.5), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 272a1e3675d361ff394988ceadd0161f Package: Category Version: 2.78.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 861fb86c9ab5fcb5b18a870d3278499c Package: categoryCompare Version: 1.56.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: b9aad00be5e6dbf19df93d21b1fe218f Package: CatsCradle Version: 1.6.1 Depends: R (>= 4.4.0) Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr Suggests: fossil, interp, knitr, BiocStyle, tictoc License: MIT + file LICENSE MD5sum: f7a82b585c9ff85f4af067d30a9a2610 Package: CausalR Version: 1.44.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8c9922f5d7d8acabc345b36446e9c4cf Package: cbaf Version: 1.34.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 61dbb98ff365825cf40060277b12f46b Package: cBioPortalData Version: 2.24.0 Depends: R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, Seqinfo, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: 4d96ec5b3102c656dfc5b9ea3a011952 Package: CBN2Path Version: 1.2.0 Depends: R (>= 4.1.0) Imports: R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr, igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks, BiocParallel Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: 3b02cdc4e2ab41ffe18ffea00002bcfc Package: CBNplot Version: 1.12.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: fa432c56eec85cfeed2aebcfd9b5112a Package: cbpManager Version: 1.20.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 23fe4c130836ad0c83f59ebbc75d28cc Package: CCAFE Version: 1.4.0 Depends: R (>= 4.4.0) Imports: dplyr, VariantAnnotation Suggests: testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges License: GPL-3 MD5sum: 76afdb8f955edd4b06bcaa58e6bd6f9e Package: ccImpute Version: 1.14.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: 62342b59b71517e574b31d29b07ce209 Package: CCPlotR Version: 1.10.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cdaa442feb60ce08aa1a9e374fb72379 Package: CCPROMISE Version: 1.38.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: fb9ceb457e9db1c55262a6bf4fb6485a Package: CDI Version: 1.10.0 Depends: R(>= 3.6) Imports: matrixStats, SeuratObject, Seurat, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: de709e69f3d93411d8bf853cb3a356ad Package: celaref Version: 1.30.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: cd6a0ba0ebf1782c28b3459b1bea159a Package: celda Version: 1.28.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize, dendextend, ggdendro, pROC LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 02cee08036fc66f8da715530d585c1e2 Package: CellBarcode Version: 1.18.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 8aac2ca7f5c8efef8b1fbe4b99f2fb85 Package: cellbaseR Version: 1.36.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: 9162eac7392b8785cd4f11659c16cb47 Package: CellBench Version: 1.28.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: b90c2295ffe89487b32a21a54824c921 Package: CelliD Version: 1.19.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: 90bf749cd453f2c3214db623dc7d33b7 Package: cellity Version: 1.40.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 86d488b4ce6a33d2da6ecf6d4fec8ec3 Package: CellMapper Version: 1.38.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: cef81366738f2fcdbc19bd6a0054a521 Package: CellMentor Version: 1.0.1 Depends: R (>= 4.5.0) Imports: methods, Matrix, BiocParallel, SingleR, Seurat (>= 4.0.0), utils, stats, parallel, progress, ggplot2, data.table, magrittr, graphics, RMTstat, sparsesvd, cluster, skmeans, MLmetrics, tibble, lsa, nnls, SingleCellExperiment, entropy, irlba, aricode Suggests: testthat (>= 3.0.0), covr, withr, rmarkdown, knitr, BiocStyle, scater, scRNAseq License: Apache License (>= 2) MD5sum: 588711a1bfef8a67e348b21153af77bb Package: cellmig Version: 1.2.0 Depends: R (>= 4.5.0) Imports: base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, utils, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat License: GPL-3 + file LICENSE MD5sum: a36925b6d558847f5536f930a65e5ca3 Package: cellmigRation Version: 1.20.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: cb3ac3e15b660cf5c8d3c42af6be0dfd Package: CellMixS Version: 1.28.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 43bb6ce5875d1844e2b5efc50e673629 Package: CellNOptR Version: 1.58.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: 20ec863e61837fe7f4f570ee238b7294 Package: cellscape Version: 1.36.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: f1e3e5f0608ec2019ea85f37e5a685a4 Package: CellTrails Version: 1.30.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: c6f1e00f50f0f571a9ba8506f2f1bfaa Package: cellxgenedp Version: 1.16.0 Depends: R (>= 4.1.0), dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 1a06953a85bee39384ab03f628c7edf3 Package: CEMiTool Version: 1.36.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: bcb4f7482992c3ad876b770c78a9fc2d Package: censcyt Version: 1.20.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: 3cec49c7acba8951bc7ba69a41cadf72 Package: Cepo Version: 1.18.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 91fe8ea4b26cec2893fa89c4f03f53ac Package: ceRNAnetsim Version: 1.24.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: b086ddf676bee22bec64498816ce6719 Package: CeTF Version: 1.24.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: e91f98c7221bc3c4711bc4e0264a291a Package: CexoR Version: 1.50.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 6d29e1ef59ca9ca4d9776b9af9bc603e Package: CFAssay Version: 1.46.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: 0a2d77cb1c8e18f5534486b0b7481b6a Package: cfdnakit Version: 1.10.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: 7d8e55f9d4020f4d23497fa4ad52a816 Package: cfDNAPro Version: 1.18.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: 9b64c42ef5d8b837415abafb1b63d2d3 Package: CGEN Version: 3.48.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: f6e75caeb95434d9471bf4cf6bf34e9b Package: CGHbase Version: 1.72.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 5570e8be330cc011453983a81c431109 Package: CGHcall Version: 2.74.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: abdf151168b9f47984d21f7272199218 Package: cghMCR Version: 1.70.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 49f9231df7a5f8dcf533d9fa085a46e8 Package: CGHnormaliter Version: 1.66.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: 789afb7e758727d5415afad551ea71f1 Package: CGHregions Version: 1.70.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 1c3c73116ef4fb15b0a52389dd8451d8 Package: ChAMP Version: 2.42.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: a280546b9fd4f299b8dcaab6a508dcb0 Package: ChemmineOB Version: 1.49.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit,codetools Enhances: ChemmineR (>= 2.13.0) License: Artistic-2.0 MD5sum: 7d49b178e54d020c5216bf79aa82a3ec Package: ChemmineR Version: 3.64.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: b9ac5b30945cc9b6b15d0e6710587911 Package: CHETAH Version: 1.28.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: 79b3cf777d99df7e536c3086c84a7474 Package: chevreulPlot Version: 1.4.0 Depends: R (>= 4.5.0), SingleCellExperiment, chevreulProcess Imports: base, cluster, clustree, ComplexHeatmap (>= 2.5.4), circlize, dplyr, EnsDb.Hsapiens.v86, forcats, fs, ggplot2, grid, plotly, purrr, S4Vectors, scales, scater, scran, scuttle, stats, stringr, tibble, tidyr, utils, wiggleplotr (>= 1.13.1), tidyselect, patchwork Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 493c721d4ed338bea0ff0c677da48cc4 Package: chevreulProcess Version: 1.4.0 Depends: R (>= 4.5.0), SingleCellExperiment, scater Imports: batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ea3b6a192b8ee974aa539642ba0a4db2 Package: chevreulShiny Version: 1.4.0 Depends: R (>= 4.5.0), SingleCellExperiment, shiny (>= 1.6.0), shinydashboard, chevreulProcess, chevreulPlot Imports: alabaster.base, clustree, ComplexHeatmap, DataEditR (>= 0.0.9), DBI, dplyr, DT, EnhancedVolcano, fs, future, ggplot2, ggplotify, grDevices, methods, patchwork, plotly, purrr, rappdirs, readr, RSQLite, S4Vectors, scales, shinyFiles, shinyhelper, shinyjs, shinyWidgets, stats, stringr, tibble, tidyr, tidyselect, utils, waiter, wiggleplotr Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86 License: MIT + file LICENSE MD5sum: e17371f8d8e4651641dd74f380868c02 Package: Chicago Version: 1.40.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: ebec6e9b3d12dd655caacad6ea471a71 Package: chihaya Version: 1.12.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 2a3eda1bafb85eb748c5ed54715594b8 Package: chimeraviz Version: 1.38.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: a3546850c90e11a3f776ac91d87ee854 Package: ChIPanalyser Version: 1.34.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: b8ab0b2cc4c9aa6218bf3855feb37f25 Package: ChIPComp Version: 1.41.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,Seqinfo,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 0ebb52202357aa00c5a281d4d384175d Package: chipenrich Version: 2.36.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 01c762d68dd3324931b5b78e3611894e Package: ChIPexoQual Version: 1.36.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.45.1) Imports: methods, utils, Seqinfo, stats, BiocParallel, GenomicRanges (>= 1.61.1), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 2.25.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 612a5431b9e597b3f4bca7ca665acbf7 Package: ChIPpeakAnno Version: 3.46.0 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: 2ea231155313ff5e24e55ed443c1a149 Package: ChIPQC Version: 1.48.3 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: 8b60ac0bc24042632161bb60ee59dc04 Package: ChIPseeker Version: 1.48.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.2.0) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a7d1592e04156fe307e3e21bc5b3b833 Package: chipseq Version: 1.62.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: e2318ad0dcdc6f495342cab680a4d36f Package: ChIPseqR Version: 1.66.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: 3482a33d2ba97c1ea958dec86a273ba8 Package: ChIPsim Version: 1.66.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 983d6461eec84335f3dda8f10c93bc3e Package: ChIPXpress Version: 1.56.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e1e7f4f814d541e25efde0616b50451e Package: chopsticks Version: 1.78.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 4b77ee2e044a3de6745c81c616e57191 Package: Chromatograms Version: 1.2.0 Depends: BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0) Imports: data.table, methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra Suggests: msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4), MsBackendMetaboLights (>= 1.3.1), pheatmap, vdiffr, IRanges, RColorBrewer License: Artistic-2.0 MD5sum: 1b9cc7433ee500a706c9df3ac33f4d38 Package: chromDraw Version: 2.42.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: baf0c275b372f874e7c8bd14742b3655 Package: ChromHeatMap Version: 1.66.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: b88d0fef5dc35cb59f041997825c2d8a Package: chromPlot Version: 1.40.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 18d9b6e192545dd90c3efa364b1be4d5 Package: ChromSCape Version: 1.22.0 Depends: R (>= 4.5) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, flexdashboard, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs2, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: 54f62d8267499442cba57a747c4e1a26 Package: chromVAR Version: 1.34.1 Depends: R (>= 3.5.0) Imports: IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, pwalign, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: c6789086a113820136ffafa3e2a84175 Package: CHRONOS Version: 1.40.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 2af48262401d9634fbddc7a7903e3f43 Package: cicero Version: 1.30.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 177853f911a88dc3da5c2c8aa500dfeb Package: cigarillo Version: 1.2.1 Depends: methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges, Biostrings Imports: stats LinkingTo: S4Vectors, IRanges Suggests: Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9873a41ba886cdf053b517e6744110fc Package: CIMICE Version: 1.20.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: 860f9721c879fd3b02fc2af9093d7878 Package: circRNAprofiler Version: 1.26.0 Depends: R(>= 4.5.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: d79c5c549dc09c5bea4279583f6b261e Package: CircSeqAlignTk Version: 1.14.0 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: eeb9e770972f67ba04f3b78009a99050 Package: CiteFuse Version: 1.24.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 1869fc15812c3b74be26986aa02f6f15 Package: ClassifyR Version: 3.15.0 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale, TOP, BiocNeighbors License: GPL-3 MD5sum: 0747057e16e85d76b0e14e295db1d729 Package: cleanUpdTSeq Version: 1.50.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: 08643f9015199a41c00aca12778e53ff Package: CleanUpRNAseq Version: 1.6.0 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: e1d1ca545972caaa5a04b6cf84c71654 Package: cleaver Version: 1.50.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 310a653765137f8526ea6d27f8f4cc84 Package: clevRvis Version: 1.12.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 2dcef30b1c5f9f90db1516b54dbae889 Package: clippda Version: 1.62.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 60dc040eb31d50250a30f41cb3ecba63 Package: clipper Version: 1.52.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: c3f55db53a3530c62a7cef5883e3a5c8 Package: cliProfiler Version: 1.18.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 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Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e2609f492a5c55318c3cdd1dff267746 Package: clusterExperiment Version: 2.32.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: 1748e0e5f62011f17f9e1b40a59d8423 Package: ClusterFoldSimilarity Version: 1.8.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 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gson (>= 0.0.7), httr, igraph, jsonlite, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.2.3) Suggests: AnnotationHub, BiocManager, DOSE, ggtangle, readr, org.Hs.eg.db, quarto, testthat License: Artistic-2.0 MD5sum: a9476a2d033571859439818c24c22c42 Package: clusterSeq Version: 1.36.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 1d3fa24050d9daef76fba63495f029df Package: ClusterSignificance Version: 1.40.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 7bbb8a550651278f9f03dd82d14fbcb8 Package: clusterStab Version: 1.84.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 29e2d14dfc97c496316f2e3edca6fdac Package: clustifyr Version: 1.24.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: 546178b08f5932bd09c7ba83b254b158 Package: ClustIRR Version: 1.10.0 Depends: R (>= 4.3.0) Imports: grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales, msa, Biostrings, RADanalysis, ggseqlogo, rBLAST LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggrepel, patchwork, 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Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: 47e83b0379c7f99d6adaa392e69f97ee Package: CNVMetrics Version: 1.16.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat, XVector License: Artistic-2.0 MD5sum: e86f86556a571ba0a6c9b3f87fe51001 Package: CNVPanelizer Version: 1.44.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: e33e535134a527b8669f21472007c14d Package: CNVRanger Version: 1.28.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: 0fd6d7e67bc5fcd189f2db08d904526b Package: CNVrd2 Version: 1.50.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: cf5c50f24ae719e13235830f6f100ebb Package: CoCiteStats Version: 1.84.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 5c5fe50f3b3f5eb6ed03ba326b296bd0 Package: COCOA Version: 2.26.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 08421967eef8481abaa3bb24f6824493 Package: codelink Version: 1.80.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: e8247619d5dc93967caf8147e2c245b0 Package: CODEX Version: 1.44.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 06e150205b980749569b825a2d3f8366 Package: CoGAPS Version: 3.32.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH, testthat Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache, xml2 License: BSD_3_clause + file LICENSE MD5sum: 9053e6b825b22042f3a964275213e5b4 Package: cogena Version: 1.46.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 138bd9825c06796f7e19a59742a89179 Package: cogeqc Version: 1.16.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 586c94e3babee8f1b19344bc311dcd34 Package: Cogito Version: 1.18.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, Seqinfo, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 7426fe7b97c64cfbada31ec2db42dae3 Package: coGPS Version: 1.56.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 3e54a4dccc3de11ffaaf94d9699824fa Package: cola Version: 2.18.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 0b366141c606472df4d4276d39e1e60c Package: comapr Version: 1.16.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 68f662679720d2a45aba58ba2341feab Package: combi Version: 1.24.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: d1166a773f432acee0d3ab3c9a3dbb50 Package: coMethDMR Version: 1.16.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 821bf4615ed744745494ba66f58e4322 Package: COMPASS Version: 1.49.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 5573f3983ece961054cea5f772621cf4 Package: compcodeR Version: 1.48.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 2ac0ffcd7d0281d793625756516bc3eb Package: CompensAID Version: 1.0.0 Depends: R (>= 4.1.0) Imports: checkmate, dplyr, flowCore, flowDensity, ggcyto, ggplot2 (>= 3.5.2), methods, ParallelLogger, reshape2, rlang, stats, tibble, tidyr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL (>= 3) MD5sum: 7aa529ab0140c4498b95b91b4c45167f Package: compEpiTools Version: 1.46.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, Seqinfo Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 93dd5ac8038e008907812f8f278b9c7a Package: ComplexHeatmap Version: 2.28.0 Depends: R (>= 4.0.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: d3a3bf5d44537f9dc9a1e9ed49cd9469 Package: CompoundDb Version: 1.16.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi, data.table Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 13dcca8334bacfa59dc506b1c151d42b Package: ComPrAn Version: 1.20.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 40282e47208f12d6c2b3733782aad3a8 Package: compSPOT Version: 1.10.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6df475893b787b5824faac7c3b8feac8 Package: concordexR Version: 1.12.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: d475f9fc6a180403560532b1cb898c72 Package: condiments Version: 1.20.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: a525ff0fb468aa04020c48194ea0d70e Package: CONFESS Version: 1.40.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: 2d1c932af0d8384047fd9ef01a270939 Package: consensus Version: 1.30.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: b6dabb4e719bc962a1284b7a9aafc75a Package: ConsensusClusterPlus Version: 1.76.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 3b3b8c23c1dcec0ced565af7b4cf949c Package: consensusOV Version: 1.34.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel Suggests: BiocStyle, ggplot2, knitr, rmarkdown, magick License: Artistic-2.0 MD5sum: 4b59cf141cd530fcedfa54ad61427ef4 Package: consensusSeekeR Version: 1.40.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: Seqinfo, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: a7d63a342e138cabc33beccb059fa72d Package: consICA Version: 2.10.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: 337c869f38bdb5d75a06ea321481d9fc Package: CONSTANd Version: 1.20.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: 9dd5b69739b412881914c64436fa9bd0 Package: conumee Version: 1.46.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, Seqinfo Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: f9057226b53899b8be5e62b52cac653f Package: convert Version: 1.88.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: 875bc995fec5f47b494ada99fbb790a7 Package: copa Version: 1.80.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: e82143ebaeccb586d8b31f16a137ce89 Package: CopyNumberPlots Version: 1.28.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 MD5sum: 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Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: 51e9e59a546158b7af95b5950379e403 Package: Cormotif Version: 1.58.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: c735f2a2248b4a2b6e6376d2f888c76c Package: corral Version: 1.22.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 MD5sum: e90f24b90c01fbaa0c3f24f74523d34c Package: coseq Version: 1.36.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 19543ed28a6bda533d9b318f62504025 Package: CoSIA Version: 1.12.1 Depends: R (>= 4.3.0), methods (>= 4.3.0), ExperimentHub (>= 2.7.0) Imports: dplyr (>= 1.0.7), magrittr (>= 2.0.1), RColorBrewer (>= 1.1-2), tidyr (>= 1.2.0), plotly (>= 4.10.0), stringr (>= 1.4.0), ggplot2 (>= 3.3.5), tibble (>= 3.1.7), org.Hs.eg.db (>= 3.12.0), org.Mm.eg.db (>= 3.12.0), org.Dr.eg.db (>= 3.12.0), org.Ce.eg.db (>= 3.12.0), org.Dm.eg.db (>= 3.12.0), org.Rn.eg.db (>= 3.12.0), AnnotationDbi (>= 1.52.0), biomaRt (>= 2.46.3), homologene (>= 1.4.68.19), annotationTools (>= 1.64.0), readr (>= 2.1.1), tidyselect (>= 1.1.2), stats (>= 4.1.2) Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) License: MIT + file LICENSE MD5sum: d363ce175b3e3bc6276a5e50df1766e9 Package: cosmiq Version: 1.46.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 49f70552d8974c1332af89e03c84dc4c Package: cosmosR Version: 1.20.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR Suggests: testthat, knitr, rmarkdown, htmltools, markdown, ggplot2, stringi, reshape2 License: GPL-3 MD5sum: baa98ea5e402fa2c4eaf53f0f8fc7182 Package: COSNet Version: 1.46.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 60fe8124b91f5009cec352e7fcf814cc Package: COTAN Version: 2.12.1 Depends: R (>= 4.3) Imports: stats, methods, grDevices, Matrix, ggplot2, ggrepel, ggdist, ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr, BiocSingular, parallelDist, ComplexHeatmap, BiocStyle, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, dendextend, zeallot, conflicted, assertthat, R.utils, withr, SummarizedExperiment, SingleCellExperiment, proxy, RSpectra, GEOquery Suggests: testthat (>= 3.2.0), proto, spelling, knitr, ragg, Cairo, data.table, gsubfn, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, cowplot, qpdf, sf, torch, S4Vectors License: GPL-3 MD5sum: 2cd7ae1fb25801800b2733faf43a1fc2 Package: countsimQC Version: 1.30.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg, rlang Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 73aaa0313a03b41ed92464afffc9db06 Package: covEB Version: 1.38.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: 75f6a8c2b520f24da42261632c877f9e Package: CoverageView Version: 1.50.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 68da329121fe0b4f7467b67ff332d74e Package: covRNA Version: 1.38.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: cd509c12f8d7c2ab58a7ff711117750e Package: CPSM Version: 1.4.0 Depends: R (>= 4.5) Imports: SummarizedExperiment, grDevices, reshape2 , survival , survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore , Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret, SurvMetrics, MASS, Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 | file LICENSE MD5sum: 615ea236e8c25cd4174ad8ba6b6442b0 Package: cpvSNP Version: 1.44.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 1d680f61654d8ccc75e3fe84210b8336 Package: cqn Version: 1.58.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg Suggests: scales, edgeR License: Artistic-2.0 MD5sum: ea010284ac5a9f5653ff7faab3cf1e14 Package: CrcBiomeScreen Version: 1.0.0 Depends: R (>= 4.3.0) Imports: rlang, methods, dplyr, doFuture, doParallel, foreach, future, future.apply, pROC, progress, progressr, stats, tibble, tidyr, TreeSummarizedExperiment, ggplot2, GUniFrac, magrittr, parallel, withr, SummarizedExperiment, caret, ranger, utils, graphics, grDevices Suggests: rstatix, MASS, mgcv, ggplotify, ggpubr, ggrepel, ggtree, glmnet, Matrix, microbiome, phyloseq, vegan, gt, testthat (>= 3.0.0), BiocManager, devtools, knitr, rmarkdown, BiocStyle, curatedMetagenomicData, xgboost License: MIT + file LICENSE MD5sum: f9bfe4f8ff5030ff55b32e19fb347334 Package: CRImage Version: 1.60.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: d01fc5abfff5114062f77005a802fd60 Package: CRISPRball Version: 1.8.0 Depends: R (>= 4.4.0), shinyBS Imports: DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap, graphics, stats, ggplot2, plotly, shinyWidgets, shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: e4b7487dea9f39dc1ffcd3a4cdd1f578 Package: crisprBase Version: 1.16.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 6e2457a7978a0131e174f69d0cbb5005 Package: crisprBowtie Version: 1.16.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), Seqinfo, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 0f60bf85063d3b1cedeb5dadf054bb04 Package: crisprBwa Version: 1.16.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), Seqinfo, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: 66526be2ae5a751e3b8cad11949543bb Package: crisprDesign Version: 1.14.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings (>= 2.77.2), BSgenome (>= 1.77.1), crisprBowtie (>= 0.99.8), crisprScore (>= 1.15.2), GenomeInfoDb (>= 1.45.7), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), IRanges, Matrix, MatrixGenerics, methods, reticulate, rtracklayer (>= 1.69.1), S4Vectors, Seqinfo, stats, txdbmaker (>= 1.5.6), utils, VariantAnnotation (>= 1.55.1) Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: 38cd0e808b1c472786beb7a19368b848 Package: crisprScore Version: 1.16.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e74966dd5a27c5c44d5a842667e04c27 Package: CRISPRseek Version: 1.52.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, Seqinfo, GenomicRanges, dplyr, keras, mltools, gtools, openxlsx, rio, rlang, stringr Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr License: file LICENSE MD5sum: afa1d709823e43f5193816d7a88163e3 Package: crisprShiny Version: 1.8.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, Seqinfo, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: ccdacdd7c3a1d50a1adbe0909db770cc Package: CrispRVariants Version: 1.40.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 23b4480d1198ca0524752ed951d791cd Package: crisprVerse Version: 1.14.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: 25ed2102a132e3adb3101192bcdfd639 Package: crisprViz Version: 1.14.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, Seqinfo, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: 9dcf1826274e80f21af99db46e1cf1c5 Package: crlmm Version: 1.70.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: 4653d085574c72873739cc0590f95236 Package: crumblr Version: 1.4.5 Depends: R (>= 4.4.0), ggplot2, methods Imports: Rdpack, viridis, tidytree, variancePartition (>= 1.36.3), SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast, dirmult Suggests: BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, reshape2, glue, tidyverse, BiocGenerics, compositions License: Artistic-2.0 MD5sum: 9e68a3e0c4f485eda540a85bd4e5cadb Package: crupR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: bamsignals, Rsamtools, GenomicRanges, preprocessCore, randomForest, rtracklayer, Seqinfo, S4Vectors, ggplot2, matrixStats, dplyr, IRanges, GenomicAlignments, GenomicFeatures, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, reshape2, magrittr, stats, utils, grDevices, SummarizedExperiment, BiocParallel, fs, methods Suggests: GenomeInfoDb, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2f5fb5c6bb7937a9fa220803fa176f1d Package: CSAR Version: 1.64.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, Seqinfo, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 06766f33118cb6c30d50e91c0ad024eb Package: csaw Version: 1.46.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1) Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 2b77e5323a151e36a82a3520e98b69e7 Package: csdR Version: 1.18.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: 3fb004f9acc56710bf526e4556f9c0a6 Package: CSOA Version: 1.2.0 Imports: dplyr, ggplot2, henna, kerntools, methods, paletteer, qs2, reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment, spatstat.utils, stats, textshape Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 42bcea10672586d2e68904f633e7dd07 Package: CSSQ Version: 1.24.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: e43fb28863c1d93776904233babce420 Package: ctc Version: 1.86.0 Depends: amap License: GPL-2 MD5sum: 278d577a1f33e3ed6dfc62f555c0b2bd Package: CTdata Version: 1.12.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: bcb9b934d9d1cc5c4f62fba02f3ac251 Package: CTDquerier Version: 2.20.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 619bf0efef58a75ccd41873d057fb5a3 Package: CTexploreR Version: 1.8.0 Depends: R (>= 4.3), CTdata (>= 1.5.3) Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: fbd20a51dd1d7a0ab24857c1bdff21b5 Package: cTRAP Version: 1.30.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs2, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: c539e4fee9cce00af6002b955c7b20ab Package: ctsGE Version: 1.38.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 45100b648b0d273b98741b33fe128d5a Package: CTSV Version: 1.14.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: 2d483c774db7a62fd1cc1c831249df4c Package: CuratedAtlasQueryR Version: 1.10.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 MD5sum: 73840f050a93badcc012678593c870e3 Package: customCMPdb Version: 1.22.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 6b4e302b05af04fd1e77ed4590771930 Package: customProDB Version: 1.51.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: bf4d49f3a5e273d07296fd484cda2ac9 Package: cyanoFilter Version: 1.20.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: 066567d74603718d4ff8fd3d30eff3ff Package: cycle Version: 1.66.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 5ed24be867a65122db038c4c7f1c4796 Package: cydar Version: 1.36.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: efff8dec1e3cf21c8336ab5d59093852 Package: cypress Version: 1.8.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: 827a0c91f941950479d8f3c6ab198ae8 Package: CytoDx Version: 1.32.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 0e46b44d6a88de726836da08cc7a4119 Package: CyTOFpower Version: 1.18.1 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 10c7a9c3d7e81d47986cc874b6baf64a Package: cytofQC Version: 2.0.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods, mixtools Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: 892f3a6167f83c39d75744a9c0b0462d Package: CytoGLMM Version: 1.20.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 7415c4f50726e89052da855decffbb45 Package: cytoKernel Version: 1.18.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: f59fdc3b522b11222a2192fd28c26465 Package: cytolib Version: 2.24.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: 093de8046ebeb8ba86a1cb6c4746db64 Package: cytomapper Version: 1.24.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 578898f94b626ba5f611e72b49995291 Package: CytoMDS Version: 1.8.0 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 506f4e865217b5f851b798b426e7f6ee Package: cytoMEM Version: 1.16.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 68ed4211e0e5a76171b1d12fd6728e4b Package: CytoML Version: 2.24.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: 4e6e3717dcb3863bf7dba8785f2c3f3e Package: CytoPipeline Version: 1.12.0 Depends: R (>= 4.4) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI License: GPL-3 MD5sum: 53cea0f7d527033779930460699bd5a2 Package: CytoPipelineGUI Version: 1.10.0 Depends: R (>= 4.4), CytoPipeline (>= 1.9.3) Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: 33b323c824615e12d895bc8f1a0e900a Package: cytoviewer Version: 1.12.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 3b239988ba995ef5a220cef880cb4313 Package: dada2 Version: 1.40.0 Depends: R (>= 4.1.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: 3992b32b4091a11f6a8a02970065a6c6 Package: dagLogo Version: 1.50.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 55996957fcbbc2d439fbcea7e80eb44f Package: daMA Version: 1.84.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 823a93e5a71856b1dfe8b52d5a5ffcdc Package: DAMEfinder Version: 1.24.0 Depends: R (>= 4.0) Imports: stats, Seqinfo, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 6450d0060fc0f8e106470191303c7dbf Package: damidBind Version: 1.0.0 Depends: R (>= 4.4.0) Imports: ggplot2, ggrepel, dplyr, tibble, stringr, tools, fs, rlang, BiocParallel, AnnotationHub, DBI, ensembldb, GenomeInfoDb, IRanges, GenomicRanges, S4Vectors, rtracklayer, limma, NOISeq, BioVenn, clusterProfiler, enrichplot, forcats, scales, colorspace, ggnewscale, methods, stats, igvShiny, shiny, DT, dbscan, circlize, ComplexHeatmap, patchwork, splines Suggests: testthat, curl, knitr, htmltools, rmarkdown, BiocStyle, bookdown, org.Dm.eg.db License: GPL-3 MD5sum: a26efe06be162c253d31f779215eb1ee Package: DaMiRseq Version: 2.24.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr, Seqinfo Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 5ed2f35e0498c873be6f1655942a6b18 Package: Damsel Version: 1.8.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: 484d42c3c17f76f26e5fb2cde7f8c681 Package: dandelionR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods, miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam, stats, SummarizedExperiment, uwot, RANN Suggests: BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, DelayedMatrixStats, slingshot, testthat License: MIT + file LICENSE MD5sum: 3248a0c2eead9af807f8568e20c057b8 Package: DAPAR Version: 1.44.0 Depends: R (>= 4.5.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, plotly, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: d9c3dfd2928456a96dd522cb8585e86c Package: dar Version: 1.8.0 Depends: R (>= 4.5.0) Imports: checkmate, cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, maaslin3, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0), GenomeInfoDb, withr License: MIT + file LICENSE MD5sum: 43df2e9061690e805e17150426202da2 Package: DART Version: 1.60.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 1226c5dec65cd6d1ae182007ce271128 Package: dcanr Version: 1.28.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 8b6aba6e82ea11ca18d1a7ae3e3ca269 Package: DCATS Version: 1.10.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: b9fc065c520003d0f5572f2a085bc109 Package: dcGSA Version: 1.40.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 6bee9ba4cca3981adbecb57c432dbaff Package: ddCt Version: 1.68.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: 66b95c723c9598da5b058394655de94e Package: ddPCRclust Version: 1.32.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: 055f85da9bf2451771a5b747725ef286 Package: dearseq Version: 1.24.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: 5237cb80d9254b11364ff1a3ccaef8a6 Package: debrowser Version: 1.40.0 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: bb482b8ef0f1a56d4bd6b88dd799914f Package: decemedip Version: 1.0.0 Depends: R (>= 4.5.0) Imports: bayesplot, cowplot, dplyr, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, matrixStats, MEDIPS, methods, purrr, R.utils, Rcpp, RcppParallel, rlang, rstan, rstantools, S4Vectors, SummarizedExperiment LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4791b8a8870f147b247ce3b5e03f60ca Package: DECIPHER Version: 3.8.1 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: 472dd9438870f08500519e9ae4bb5646 Package: decompTumor2Sig Version: 2.28.0 Depends: R(>= 4.0), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, Seqinfo, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 91414c98ec1e6d63e4758725c67e3c1a Package: DeconRNASeq Version: 1.53.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: a48d9317df30eb157eb635de90146cbb Package: decontam Version: 1.32.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 980a4c9c01bf38c41895b3d3aa7040c0 Package: decontX Version: 1.10.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9b6bbc14c24d8bb46e5de8e8f61401f6 Package: DeconvoBuddies Version: 1.4.0 Depends: R (>= 4.4.0) Imports: AnnotationHub, BiocFileCache, BiocParallel, DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, ggrepel, graphics, grDevices, MatrixGenerics, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils Suggests: Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse License: Artistic-2.0 MD5sum: cd1de30c0611e913431c8ac7145bb2c2 Package: deconvR Version: 1.18.0 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: 0a92f6a3dd088ada29564f9fec7dc0a0 Package: decoupleR Version: 2.17.0 Depends: R (>= 4.0) Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick License: GPL-3 + file LICENSE MD5sum: 9fec6baf51b27f31d46241c1d44f0fe6 Package: DeeDeeExperiment Version: 1.2.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, writexl, cli Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, ExperimentHub, scater, muscat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: dd7c841d5b0b7fd574533d8745ce87a7 Package: DeepPINCS Version: 1.20.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 6626a19232e4e7f9b11c812662a42845 Package: deepSNV Version: 1.58.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: bfe0c26cbb3683c0827fc94f93f24c97 Package: DeepTarget Version: 1.6.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 870397003ce939234675f0a03387cc53 Package: DEFormats Version: 1.40.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: 86d6e4a92083a5c8bf18039d3fed96cd Package: DegCre Version: 1.8.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, Seqinfo, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 703fc1a0ff400cec676494b4f41b04d8 Package: DegNorm Version: 1.22.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 2bed4a7d45c4cadd5ffeb2cd3cd290e1 Package: DEGraph Version: 1.64.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: 5320e42e3fb38f8eb914ada8d752bd85 Package: DEGreport Version: 1.48.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: f4f84591e95b4970d6298a6e7d040d04 Package: DEGseq Version: 1.66.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 35d3460d61fc4dcef66e81ca60c402de Package: DelayedArray Version: 0.38.2 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6), IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>= 1.7.5) Imports: stats Suggests: BiocParallel, HDF5Array (>= 1.17.12), ZarrArray, genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 66f7d947d935f84de1cf7c954ff44f15 Package: DelayedDataFrame Version: 1.28.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: 798ec0640afdfde78bebf2fe0734cfde Package: DelayedMatrixStats Version: 1.34.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>= 1.5.19) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: 06e0ee0fd766b055e97e6a1a3a220c4a Package: DelayedRandomArray Version: 1.20.0 Depends: SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 8d68694468f25dd1019dfcb862b262bb Package: DelayedTensor Version: 1.18.0 Depends: R (>= 4.1.0) Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: 74efdfdabb2715ee2f460dc40ab70105 Package: DELocal Version: 1.12.0 Imports: DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2, matrixStats, stats Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle License: MIT + file LICENSE MD5sum: 3905c6f494d4829243fb6cfc4eff6829 Package: deltaCaptureC Version: 1.26.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 31ba2970eae0d70c414f810638492315 Package: deltaGseg Version: 1.52.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 8e5723e4509f692f1178c770acb33758 Package: DeMAND Version: 1.42.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 98d6e32adbc4c7eb5cf40ea734df6061 Package: DeMixT Version: 2.0.0 Depends: R (>= 4.0.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment Imports: matrixStats, stats, truncdist, base64enc, ggplot2, KernSmooth, matrixcalc, sva, dendextend, fitdistrplus, pbapply, psych, magrittr, graphics, grDevices, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, calibrate, BiocStyle License: GPL-3 MD5sum: 05569811a1f375d66c0dce8eea134c9d Package: demuxmix Version: 1.14.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e348871204b3f4024d1961198fe35053 Package: demuxSNP Version: 1.10.0 Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports: MatrixGenerics, BiocGenerics, class, Seqinfo, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat License: GPL-3 MD5sum: 8d36fb8025d08e0769d4bd1852f34b44 Package: DenoIST Version: 1.0.0 Depends: R (>= 3.5.0) Imports: flexmix, hexbin, pbapply, sparseMatrixStats, SpatialExperiment, stats, SummarizedExperiment, parallel, Matrix, dbscan, methods Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, patchwork License: MIT + file LICENSE MD5sum: 2a820a69080b6cc8478e8cc3fc68c780 Package: densvis Version: 1.22.0 Imports: Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat License: MIT + file LICENSE MD5sum: 2067afb166c3e34605ffd36fd03ad988 Package: DepecheR Version: 1.28.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 186930584dfce90797566b9569eee2b4 Package: DepInfeR Version: 1.16.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm License: GPL-3 MD5sum: 90e8a47b667ee6d5b223219ea69ce934 Package: DEqMS Version: 1.30.0 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,dplyr,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 9c82e30a919254cf52d3961cca69a52d Package: derfinder Version: 1.46.0 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.61.1), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 2.25.1), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 7fa8fbe41c4c8314f6b6010a81350d7e Package: derfinderHelper Version: 1.46.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 MD5sum: c612d7e2220eef5bb114e4e7a94dcee1 Package: derfinderPlot Version: 1.46.0 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), Seqinfo, GenomeInfoDb (>= 1.45.9), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 443167b56f90e2d7b4def8230904f2bc Package: DEScan2 Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, Seqinfo, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: 4656d811a08858a379a7dd3e4492d697 Package: DESeq2 Version: 1.52.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: b60bf070204f274aa8c2e33a135d6bc8 Package: DEsingle Version: 1.32.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: c9a578ae2d8836f4951e85926bc0ee96 Package: DESpace Version: 2.4.0 Depends: R (>= 4.5.0) Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel, methods, scales, scuttle Suggests: knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub, spatialLIBD, purrr, reshape2, tidyverse, concaveman License: GPL-3 MD5sum: b4d8d70d63f7c2dab4e74a5de304280c Package: destiny Version: 3.26.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 MD5sum: f79958303ee610e1045d36c0be0f2a4d Package: DEsubs Version: 1.38.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: 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LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, rtracklayer, grid License: Artistic-2.0 MD5sum: 7e9cbe1b3979bdbb6e090adf0de4a887 Package: diffcoexp Version: 1.32.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: 11e3d99f90ea1ec25596c304ad0b2e9e Package: diffcyt Version: 1.32.1 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: da66048d0e7772f635dd894efd1558d6 Package: DifferentialRegulation Version: 2.10.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, 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SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: 3ff05db10f84c4dd5ab58311883c8f28 Package: dittoSeq Version: 1.24.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran, MASS License: MIT + file LICENSE MD5sum: e28491711e039d7d7a7f9c00fb69f3e4 Package: divergence Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 300dd4c7b7e104bb8007652e444bdffb Package: dks Version: 1.58.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 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IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit License: Artistic-2.0 MD5sum: f111a3576fd023ec5c014fbc0c6f06e9 Package: DMRcaller Version: 1.44.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils, Rsamtools, GenomicRanges, GenomicAlignments, Biostrings, BSgenome, BiocManager, S4Vectors, IRanges, InteractionSet, stringr, inflection, BiocParallel, Seqinfo, GenomeInfoDb Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 MD5sum: 33285a602c4a0ca380dc66aacd597caf Package: DMRcate Version: 3.8.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 40b730866c654573f82cf537d05d75f8 Package: DMRScan Version: 1.34.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 3072b3864727de96f3340794fef8ae2a Package: dmrseq Version: 1.32.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, Seqinfo, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 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SummarizedExperiment, dplyr, rlang, ggforce, geomtextpath, ggplot2 Suggests: BiocStyle, airway, tidyverse, knitr, rmarkdown, testthat (>= 3.0.0), dominatRData License: MIT + file LICENSE MD5sum: 515b25effc700cd1146650b1bf8e637a Package: DominoEffect Version: 1.32.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, Seqinfo, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 5f07587a34d6a09f09226ec2d301b3a6 Package: dominoSignal Version: 1.6.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 89b54dd1d76ca941d928130d0be74014 Package: doppelgangR Version: 1.40.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: b09a7933a73be15905adc90c1a2baa1d Package: Doscheda Version: 1.34.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 22f160a975c479beb71e287ad81b02df Package: DOSE Version: 4.6.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim (>= 2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: ed6bd919a296f7f2f3dbfb590fde9d9d Package: doseR Version: 1.28.0 Depends: R (>= 3.6) Imports: 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rmarkdown, testthat, withr, magick License: MIT + file LICENSE MD5sum: bf738b68a40ad510fe500d6245a2cdff Package: doubletrouble Version: 1.12.0 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 04d29f6ca4ced2385a50b245afe05550 Package: drawProteins Version: 1.32.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 431749beefb85afd4ae0e0ad29637d5a Package: dreamlet Version: 1.10.0 Depends: R (>= 4.3.0), variancePartition (>= 1.36.1), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, reformulas, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle License: Artistic-2.0 MD5sum: ed20a46096cc20592b8025cd4c8213e9 Package: DRIMSeq Version: 1.40.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 0cd80900d7768c5933df3321d78b80b5 Package: DriverNet Version: 1.52.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: abea7e1360dbbe18e66fc975cd1328a4 Package: DropletUtils Version: 1.32.0 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle (>= 1.21.4) LinkingTo: Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: 6b25e5f6224e1f9172935571730d7ffa Package: drugfindR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: tibble, rlang, dplyr, purrr, readr, stringr, stats, lifecycle, S4Vectors, httr2, curl, DFplyr Suggests: AnnotationDbi, BiocStyle, biocthis, codemetar, devtools, here, httptest2, jsonlite, knitr, rmarkdown, testthat (>= 3.0.0), tidyverse, usethis License: GPL-3 + file LICENSE MD5sum: 97c2ebe9c7d1942e7937a65188bd9ca1 Package: drugTargetInteractions Version: 1.20.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: 5a1803be5c588ffc30ba82c8cc8a2c8a Package: DrugVsDisease Version: 2.54.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 MD5sum: b837ba50e64448cc556de55303f16d12 Package: DspikeIn Version: 1.2.0 Depends: R (>= 4.1.0) Imports: ape, Biostrings, data.table, DECIPHER, DESeq2, dplyr, edgeR, flextable, ggalluvial, ggnewscale, ggplot2, ggpubr, ggraph, ggrepel, ggridges, ggtree, ggtreeExtra, graphics, grDevices, igraph, limma, matrixStats, methods, microbiome, officer, grid, reshape2, patchwork, phangorn, phyloseq, randomForest, RColorBrewer, rlang, S4Vectors, scales, stats, tibble, tidyr, SummarizedExperiment, TreeSummarizedExperiment, utils, msa, xml2, ggstar Suggests: Biobase, mia, BiocGenerics, magrittr, BiocManager, cluster, devtools, DT, e1071, foreach, ggtext, intergraph, knitr, optparse, plyr, preprocessCore, qpdf, remotes, rmarkdown, ShortRead, testthat (>= 3.0.0), vegan, viridis License: MIT + file LICENSE MD5sum: 54a787ad26365edf48ecf1db09c2a005 Package: DSS Version: 2.60.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: 50ce2dc0b848307cb7ee291d2537540b Package: dStruct Version: 1.18.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: b409bd0ac63f90b1705ca82b98655d56 Package: DTA Version: 2.58.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: 1d52bd4cb9e95fda8a33bfe364fafeb9 Package: Dune Version: 1.24.0 Depends: R (>= 3.6) Imports: BiocParallel, SummarizedExperiment, 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RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite,codetools License: Artistic-2.0 MD5sum: f0248685e7ee3b04997b25f1b32688fb Package: eisaR Version: 1.24.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer, withr License: GPL-3 MD5sum: 48f9fc5ba41a9908bac09e6f52405bda Package: ELViS Version: 1.4.0 Depends: R (>= 4.5.0) Imports: reticulate, BiocGenerics, circlize, ComplexHeatmap, data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2, glue, graphics, grDevices, igraph, IRanges, magrittr, memoise, methods, parallel, patchwork, scales, segclust2d, stats, stringr, txdbmaker, utils, uuid, zoo Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f6be9df9f4435609600f5e181fd17530 Package: EMDomics Version: 2.42.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: e431b276d1cff465e7c5f2fb76a45047 Package: EmpiricalBrownsMethod Version: 1.40.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: f370e380ea0a5db3feb354c605495a3c Package: EnhancedVolcano Version: 1.30.0 Depends: ggplot2, ggrepel Imports: methods, scales, grid, grDevices Suggests: RUnit, ggrastr, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 MD5sum: 18a622e961af48ec12261d7d58a54e5d Package: enhancerHomologSearch Version: 1.18.0 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, Seqinfo, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: GenomeInfoDb, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) MD5sum: de086c6c06fe3e8e7dcaac24a3df3bb7 Package: EnMCB Version: 1.24.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: 832665175ef757a808b935dcefcf42eb Package: ENmix Version: 1.48.3 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 55efce9d3dce97f18eb05490613712bb Package: EnrichDO Version: 1.6.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, Rgraphviz, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, tidyr, stats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 5cd9f376dc8b8056e95d6d95997a3a18 Package: EnrichedHeatmap Version: 1.42.0 Depends: R (>= 4.0.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: efa33f9f9394b9b341225602c4568cab Package: EnrichmentBrowser Version: 2.42.0 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: 27a542f0f3cd4f248d60f1f7062d9fdf Package: enrichplot Version: 1.32.0 Depends: R (>= 4.2.0) Imports: aplot (>= 0.2.1), DOSE, dplyr, enrichit, ggfun (>= 0.1.7), ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle (>= 0.0.9), ggtree, GOSemSim (>= 2.37.2), graphics, grid, igraph, methods, purrr, RColorBrewer, reshape2, rlang, scatterpie, stats, tidydr, utils, yulab.utils (>= 0.2.2) Suggests: AnnotationDbi, clusterProfiler, europepmc, ggarchery, ggforce, ggHoriPlot, ggplotify, ggridges, ggstar, ggtreeExtra, ggupset, glue, grDevices, gridExtra, gson, org.Hs.eg.db, quarto, scales, tibble, tidyr License: Artistic-2.0 MD5sum: b6e6bdb2baca382580cf63d118ff49ba Package: enrichViewNet Version: 1.10.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, igraph, reshape2, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, scatterpie, ggtangle, ggrepel, testthat, ggnetwork, magick License: Artistic-2.0 MD5sum: ae3faadc6f592e55830ea784bb4f0260 Package: ensembldb Version: 2.36.1 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 45c83e1b47c26df42c2c28a0a36688bd Package: epialleleR Version: 1.20.0 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: db9806ba932e1005c99875c67b4d21e7 Package: EpiCompare Version: 1.16.0 Depends: R (>= 4.2.0) Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges (>= 2.41.3), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis License: GPL-3 MD5sum: 8d8df94b6b3df54fb3fe752ea0702cee Package: epidecodeR Version: 1.20.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 78b36f2270ee7f2b17c177426704fcf6 Package: EpiDISH Version: 2.28.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix, genefilter Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 04270ae4bc860f18dff221324ee268c5 Package: epigenomix Version: 1.52.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: 406c5ce4762c361cf8797231ee6d384f Package: epigraHMM Version: 1.20.2 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, gcapc, genomationData License: MIT + file LICENSE MD5sum: 35c4afe7b2655886071a6d3b96b871db Package: EpiMix Version: 1.14.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: be1cad2e025f208c4211cbd23a1fe92f Package: epimutacions Version: 1.16.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 14e5601b7639cf4e34f2ca9ea180e227 Package: epiNEM Version: 1.36.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: 493a7e33222663ce431ce648c8d0b530 Package: EpipwR Version: 1.6.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: a2298cf241a74e96ecf2c8a47aa2ad13 Package: epiregulon Version: 2.2.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, AnnotationHub, GenomeInfoDb, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, scrapper LinkingTo: Rcpp Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, scMultiome License: MIT + file LICENSE MD5sum: c9e9362b2fbfde20929572ea24a8d03c Package: epiregulon.extra Version: 1.8.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: dd40821fee893fab8c69d827dd628767 Package: epiRomics Version: 1.0.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi (>= 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tidyr, utils, yulab.utils (>= 0.2.0), grid Suggests: ape, BSgenome, BSgenome.Hsapiens.UCSC.hg38, clusterProfiler, data.table, GEOmetadb, GEOquery, gggenes, ggimage, ggiraph, ggplotify, ggtree, gginnards, gridBase, gtools, ggupset, ggVennDiagram, JASPAR2024, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat, TFBSTools, TxDb.Hsapiens.UCSC.hg38.knownGene, universalmotif License: Artistic-2.0 MD5sum: b6442b11128b35db9d3b4667b7441520 Package: epistack Version: 1.18.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: ed644ce2f3dd94adc142e83b3b6da8b5 Package: epistasisGA Version: 1.14.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 68cad17349117d127ebda5ef5cdb2a0c Package: EpiTxDb Version: 1.24.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, Seqinfo, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 6ece892570061bd8548c3e50f5c16c2e Package: epivizr Version: 2.42.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 61cf2baeb5fbbbff0981c8bb48b021b9 Package: epivizrChart Version: 1.34.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 5b1852bc950b49d1c1c4da3b4f368192 Package: epivizrData Version: 1.40.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), OrganismDbi, GenomicFeatures (>= 1.61.4), Seqinfo, IRanges, ensembldb (>= 2.33.1) Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: a96b858b6646b3cb06c8aa95bbaced68 Package: epivizrServer Version: 1.40.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 7e2f5bd16898eef3af3cf2da0055c8b9 Package: epivizrStandalone Version: 1.40.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, Seqinfo, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: 055971ccd1e084d21f9cb2e51aa428b0 Package: erccdashboard Version: 1.46.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 25ec64ba420c1042dc6cc2859a7a6cc4 Package: ERSSA Version: 1.30.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 79ffa6186ed44e945885c0e9d562f957 Package: esATAC Version: 1.34.0 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, Seqinfo, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: beef8ffec2e8ff432c87592402c658b8 Package: escape Version: 2.8.0 Depends: R (>= 4.1) Imports: ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics, methods, stats, SummarizedExperiment, utils Suggests: AUCell, BiocParallel, BiocStyle, DelayedMatrixStats, dplyr, fgsea, GSEABase, ggraph, ggridges, ggpointdensity, GSVA, hexbin, igraph, irlba, knitr, msigdb, patchwork, rmarkdown, rlang, scran, SeuratObject, Seurat, SingleCellExperiment, spelling, stringr, testthat (>= 3.0.0), UCell License: MIT + file LICENSE MD5sum: fd418f4a9b2cc0c66c181a7af54412cc Package: escheR Version: 1.12.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 90106257e89445f4f7986b67c820b6a2 Package: esetVis Version: 1.38.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 0c671eb2df3f2a88e8e6faf3ee776a7e Package: eudysbiome Version: 1.42.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 4f5980903e7f0d3ec5c5c22ee95d5497 Package: evaluomeR Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 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PharmacoGx, data.table, futile.logger, gDRutils (>= 1.7.1), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx, qs2 Suggests: BiocStyle, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1), knitr, purrr, testthat License: Artistic-2.0 MD5sum: 0c41e1fbe7d939e74aeb9c20699a3988 Package: gDRstyle Version: 1.10.0 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, BiocStyle, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: knitr, pkgdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: a7b8d5cf4efcac05145b3039ffced770 Package: gDRutils Version: 1.10.0 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, digest, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment, qs2, utils Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.7.1), gDRtestData (>= 1.7.1), IRanges, knitr, lintr, mockery, purrr, rcmdcheck, rmarkdown, scales, testthat, tools, withr, yaml License: Artistic-2.0 MD5sum: b8d678a61ffde29d0a09139b52f8640b Package: GDSArray Version: 1.32.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: e0fee023598ab510c900889913e88e2a Package: gdsfmt Version: 1.48.2 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 10d1280b5d487982bd64c8a35544c6bd Package: GeDi Version: 1.7.1 Depends: R (>= 4.4.0) Imports: Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, expm, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, methods, circlize, proxyC, simona Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, mosdef, GeneTonic, htmltools, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: d65fb6e71fd9d5651e651d035be6ea37 Package: GEM Version: 1.38.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: b97c27ec687a6e4e685025d2bc6861e8 Package: gemini Version: 1.26.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 65a4eb6b899ac016f0a4cf5d964db7f4 Package: gemma.R Version: 3.8.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, kableExtra, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny License: Apache License (>= 2) MD5sum: ccf03096b7ca2b7f5ec4f702b5b5ef1c Package: genArise Version: 1.88.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: bfaddc12a4c048d1429d5cc0cd38d1c1 Package: geneAttribution Version: 1.38.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, Seqinfo, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e370850b9458a5c6d856f8bfbe485856 Package: GeneBreak Version: 1.42.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 816ec186576e173cf1f8ccce40605f07 Package: geneClassifiers Version: 1.36.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 51d9af5d06748b91fa7a413ebd4b36bf Package: GeneExpressionSignature Version: 1.58.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 48a1a76a2bf189a506de428a82e0ca6c Package: genefilter Version: 1.94.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 438edb00ea4faa1c7eeac95abf0880cc Package: genefu Version: 2.44.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 6a06854aa51e689ec71b864c0674e57c Package: GeneGA Version: 1.62.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: e2095b6e715b79249cfc5aed07091fc4 Package: GeneMeta Version: 1.84.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 0dace69b230c27ccab77510eae064017 Package: GeneNetworkBuilder Version: 1.54.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: 8a04dc5040beef496a168475dcd91788 Package: GeneOverlap Version: 1.48.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 414143e2950362ebf2d24b8aac053e29 Package: geneplast Version: 1.38.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 0bff84e9df0ecadf34698ffd9803061c Package: geneplotter Version: 1.90.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 64c38a75ba57ab0cf1481058c97cad1d Package: geneRecommender Version: 1.84.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 47005ff7490022be44fb63ac10f1c9fa Package: GeneRegionScan Version: 1.68.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 165726801b492ed0c52cfaa5b5a83b22 Package: geneRxCluster Version: 1.48.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 69f757d59356506d2783147095673fa8 Package: GeneSelectMMD Version: 2.56.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 80b16557c4c3b458c08a46791afc2f5b Package: GENESIS Version: 2.42.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb License: GPL-3 MD5sum: e003d12edd288aa2158bca4e7d7076ac Package: GeneStructureTools Version: 1.32.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: f83cfc70d76c2530449cbe86833a7734 Package: geNetClassifier Version: 1.52.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: ea09b3813e31787681f51c8ad66a985d Package: GeneticsPed Version: 1.74.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: ef0cbb5700ff6165dc08eca713e09af1 Package: GeneTonic Version: 3.6.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 84fc670c9573f56812b234b289df6712 Package: GENIE3 Version: 1.34.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 54a482c56801375b527ff0f362281a77 Package: genomation Version: 1.44.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 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IRanges (>= 2.41.1), Seqinfo (>= 0.99.2) Imports: stats, utils, UCSC.utils Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8cb2bf3c0541f911b296ba792e0db3bf Package: genomeIntervals Version: 1.68.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: b3705f47b2ff7234f0500da026714dd8 Package: genomes Version: 3.42.0 Depends: readr, curl License: GPL-3 MD5sum: c86cbfd6eaf2dca412b05940e6a50f0a Package: GenomicAlignments Version: 1.48.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo (>= 0.99.2) LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: b1c7b96083a3db85a2e4a359054d2115 Package: GenomicCoordinates Version: 1.0.0 Depends: R (>= 4.5), GenomicRanges, IRanges Imports: S4Vectors, Seqinfo, InteractionSet, methods, plyranges, plyinteractions Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: a88721c0ed36aec7cbdbcd2ebb5ba393 Package: GenomicDataCommons Version: 1.36.0 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: 5d816c22e40a04a1615f2084f3935bad Package: GenomicDistributions Version: 1.20.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: 5acad81f90934c817710b6a1b665eeea Package: GenomicFeatures Version: 1.64.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.47.6), IRanges (>= 2.37.1), Seqinfo (>= 0.99.2), GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2), rtracklayer (>= 1.69.1) LinkingTo: S4Vectors, IRanges Suggests: GenomeInfoDb, txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 6c4caee0ed27f5186d4c2f4f432c664f Package: GenomicFiles Version: 1.48.0 Depends: BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>= 1.55.1) Suggests: BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats License: Artistic-2.0 MD5sum: 066eecfad985ee9c1d424f24559a5ec8 Package: genomicInstability Version: 1.18.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: c9da80cf20e863c7c80afae5989e95df Package: GenomicInteractionNodes Version: 1.16.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, Seqinfo, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: a8a7ab8a2017724f3c71a69835b7007c Package: GenomicInteractions Version: 1.46.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 0f37f3164ceeab8363c106505882f9f4 Package: GenomicOZone Version: 1.26.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, Seqinfo, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: ef78bbbb34419e99a665db44cd20eb49 Package: GenomicPlot Version: 1.10.0 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments 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BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart51, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 17433a1105c6933a6364357146932166 Package: GenomicScores Version: 2.24.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 83daed20ec4dffd4a0ff240247d004fe Package: GenomicSuperSignature Version: 1.20.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 91c683ca78d5808be51fbcf82784e8b7 Package: GenomicTuples Version: 1.46.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: 1304207432b9e4d77d9ae112321f217b Package: GenProSeq Version: 1.16.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 5c51377b9ef1794095c6117a48ad3214 Package: GenVisR Version: 1.44.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, Seqinfo, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: d853b0f6cdab5d4c497c1c15e513b584 Package: GeoDiff Version: 1.18.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 076c736307f95367e47c4e23e5b4bb55 Package: GEOfastq Version: 1.20.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 90e6422106a3a14ecfc21b80f6311938 Package: GEOmetadb Version: 1.74.0 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: d1a1b6838f1df911f53b9886468cf67c Package: geomeTriD Version: 1.6.0 Depends: R (>= 4.4.0) Imports: aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 169a8682b5caeab6b4796766ffcb15a8 Package: GeomxTools Version: 3.16.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: 2b59a2dd7ea8a58aad9e2070b1e00ce9 Package: GEOquery Version: 2.80.0 Depends: R (>= 4.1.0), methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, DropletUtils, SingleCellExperiment License: 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SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 5359583d24dfe7eaaff14cd8767ad3ad Package: geva Version: 1.20.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: b8e0d9a7f702dee1242f98d5702787c9 Package: GEWIST Version: 1.56.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 2492ccea3be342ae33db420322b66f02 Package: geyser Version: 1.4.0 Depends: R (>= 3.5.0) Imports: bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, cowplot, dplyr, DT, ggbeeswarm, ggplot2, ggrepel, ggh4x, htmltools, magrittr, pals, RColorBrewer, rlang, R.utils, shiny, shinyjs, S4Vectors, SummarizedExperiment, tibble, tidyselect, tidyr, yaml Suggests: airway, knitr, DESeq2, rmarkdown, stringr, testthat (>= 3.0.0) License: CC0 MD5sum: 563ce3a7f22df25ce2458c709f9b7dc2 Package: gg4way Version: 1.10.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr License: MIT + file LICENSE MD5sum: 2f9fa4114e4da0ac38765b24fe9f080d Package: ggbio Version: 1.60.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome (>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>= 1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 80dcbba96a22e84998546cf689a52ed1 Package: ggcyto Version: 1.40.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: bf5d0b02b86d506202ec796be952d63a Package: ggkegg Version: 1.10.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 32a9227393cf81779992e06983d6ef41 Package: ggmanh Version: 1.16.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: 889fd1bd3c9991d27297133911aa9843 Package: ggmsa Version: 1.18.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat (>= 3.0.0), yulab.utils License: Artistic-2.0 MD5sum: 0f1360918aa85be314186f763f0c4efd Package: GGPA Version: 1.24.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 1e4408bcf613bbd590571929ec03c5a2 Package: ggsc Version: 1.10.1 Depends: R (>= 4.1.0) Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 09c49f1abbb7ab0bbe15dd2f6505624a Package: ggseqalign Version: 1.6.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 567a36b3ee5bbd19e1ea759a9421acca Package: ggspavis Version: 1.18.1 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, OSTA.data, VisiumIO, arrow, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 81f5c535fa51b8b349ad7d4033d1f71f Package: ggtree Version: 4.2.0 Depends: R (>= 4.2.0) Imports: ape, aplot, cli, dplyr, ggfun (>= 0.1.7), ggiraph (>= 0.9.1), ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, scales, stats, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, yulab.utils (>= 0.2.3) Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, igraph, testthat, tibble, glue, Biostrings License: Artistic-2.0 MD5sum: 965f2848897c3bc6ee6f46f553eac4a6 Package: ggtreeDendro Version: 1.14.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: 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License: GPL-3 + file LICENSE MD5sum: bb0bd03aa776723285bce690db296e2a Package: gINTomics Version: 1.8.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize, MethylMix, shinyjs Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 974b2602f366ee480f34bb65a7a9f4cd Package: GLAD Version: 2.76.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 7767b8273aa9acb2b0006a944aef3a7f Package: GladiaTOX Version: 1.28.0 Depends: R (>= 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RcppArmadillo, beachmat, assorthead Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, dplyr License: GPL-3 MD5sum: 046fc6f683dd6f27d3667259719f4c54 Package: glmSparseNet Version: 1.30.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 MD5sum: 777bb69d7717ebd22baeb39d94afd272 Package: GlobalAncova Version: 4.30.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: b17fc25b9ba3a2abcea4cffee889098d Package: globalSeq Version: 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testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: fa19877278bd240837d91c6b12cbd8da Package: gmapR Version: 1.54.0 Depends: R (>= 2.15.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel, BiocIO Suggests: GenomeInfoDb, RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 692ee2ddba120957cb3d6df7ba1c0481 Package: GmicR Version: 1.26.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 35dc0f0f19190a1956d637ee4abda785 Package: gmoviz Version: 1.24.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, Seqinfo, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager, GenomeInfoDb License: GPL-3 MD5sum: 9d0fdcbe0cac6377e2f73f1a3b47c6c1 Package: GMRP Version: 1.40.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 89582e8b9031893761a86ccc092cffe1 Package: GNET2 Version: 1.27.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 0d6e668c020cfa41e91686e3ac09b6a2 Package: GNOSIS Version: 1.10.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 2d630abc20183fe9a57bf1f695074fb0 Package: GOaGO Version: 1.0.1 Depends: R (>= 4.4.0), methods Imports: AnnotationDbi, BiocGenerics, BiocParallel, clusterProfiler, data.table, DOSE, GenomeInfoDb, GenomicRanges, ggplot2, ggridges, Matrix, qvalue, S4Vectors Suggests: BiocStyle, GenomicInteractions, ggrepel, knitr, org.Hs.eg.db, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 0dd8ba67534167d949bbf0abfe71d27f Package: goatea Version: 2.0.0 Depends: R (>= 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Version: 1.46.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: 13a7258199bcf34901b0fd63c426928d Package: GOfan Version: 1.0.0 Depends: R (>= 4.5.0), ggplot2 Imports: AnnotationDbi, grid, grDevices, GO.db, igraph, methods, plotly, rlang, stats, scales, vctrs Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Dr.eg.db License: GPL-3 MD5sum: f4ac4a4a2c3573ca45209f2af7da1a11 Package: GOfuncR Version: 1.31.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 743a653dd931c6d2720338be554b3a95 Package: GOpro Version: 1.38.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 82ea7e7438728bc835c37f0381316d8b Package: goProfiles Version: 1.74.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 518cd4a70a2ddc9274e7053a48bfd06b Package: GOSemSim Version: 2.38.3 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, stats, utils, yulab.utils (>= 0.2.3) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 312be76763c92eea01bb9fb5d89aebb8 Package: goseq Version: 1.64.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, Seqinfo Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: 8f904f195e68cfac69a0dde769d60db9 Package: goSorensen Version: 1.14.0 Depends: R (>= 4.4) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick License: GPL-3 MD5sum: a6ed6f9310ce5d1784f27211bd2359b6 Package: goSTAG Version: 1.36.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 94232c623dacd7a874cd75de990f9960 Package: GOstats Version: 2.78.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 6cc25c439bcfd440d39726926dd9aaec Package: GOTHiC Version: 1.48.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, Seqinfo Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: a61a95eaeed22b87e445eb819e0d00e7 Package: goTools Version: 1.86.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 2ea73687b17680c4fdb724ef437cb452 Package: GPA Version: 1.24.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: ea8feefe3ce069f4ad30202d7693b71a Package: gpls Version: 1.84.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 29f443c2795f79135d1bfdd725832b58 Package: GrafGen Version: 1.8.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 86101664c8f915efaf4b71e2a502b7cd Package: GRaNIE Version: 1.16.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 MD5sum: f1a740bf19d33527648fa879b5d9777c Package: graper Version: 1.28.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: e43e0121f0d6e66a976046e79a70f0ec Package: graph Version: 1.90.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: eef48a0ef1520604953cb250ba8abe10 Package: GraphAlignment Version: 1.76.0 License: file LICENSE License_restricts_use: yes MD5sum: e3e58951df882c40641b16b2f14a7c07 Package: GraphAT Version: 1.84.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 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abdiv, CSOA, decoupleR, dplyr, escape, fabR, ggplot2, ggrepel, GSVA, hammers, henna, jaccard, lsa, Matrix, MLmetrics, methods, mltools, pagoda2, paletteer, reshape2, rlang, scLang, singscore, SiPSiC, stringr, stats, VAM, withr Suggests: AUCell, BiocStyle, knitr, qs2, ranger, rmarkdown, rpart, scater, scRNAseq, scuttle, Seurat, testthat (>= 3.0.0), UCell License: MIT + file LICENSE MD5sum: 25c1b384606ab08ad5d5c380f5e986a0 Package: GSALightning Version: 1.40.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 2336785f3354c8147cd1865829640414 Package: GSAR Version: 1.46.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 46ca131ae8d5324a07774964e6e9d6c7 Package: GSCA Version: 2.42.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: bfca22957f1b7ad0d75b9da87b1b2192 Package: gscreend Version: 1.26.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 0d03b276f46c1f02791f4d266e21e17e Package: GSEABase Version: 1.74.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: 61b1ac1e9b6fe77b2a41f8d7144bc622 Package: GSEABenchmarkeR Version: 1.32.0 Depends: R (>= 4.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: ce2d0cc1380399065d1fbe33bf74c9f2 Package: GSEAlm Version: 1.72.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 1b6239cd4b25b1b7239d1b99f038b78f Package: GSEAmining Version: 1.22.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: 2bcf630500bb2a57d5b38564fd609c21 Package: gsean Version: 1.32.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: adb9e3e143e7f869863a761be4bbb91c Package: GSgalgoR Version: 1.22.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 252d5b4fc555d8f029e08e4ee4e449b8 Package: GSReg Version: 1.46.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: dea99fea841def71d8043589a95eab13 Package: GSRI Version: 2.60.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: 0d015630626a976f2274eb1322d14cec Package: GSVA Version: 2.6.6 Depends: R (>= 4.0.0) Imports: methods, stats, utils, graphics, BiocGenerics, MatrixGenerics, S4Vectors, S4Arrays, HDF5Array, SparseArray, DelayedArray, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), DelayedMatrixStats, BiocParallel, SingleCellExperiment, BiocSingular, SpatialExperiment, sparseMatrixStats, cli, memuse LinkingTo: cli Suggests: RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, sva, ExperimentHub, TENxPBMCData, TENxVisiumData, spatialLIBD, scrapper, bluster, igraph, ggspavis, patchwork, ggplot2, shiny, shinydashboard, data.table, plotly, future, promises, shinybusy, shinyjs License: Artistic-2.0 MD5sum: 4a727d9c23167141ed0ffc5bc5603f3f Package: gtrellis Version: 1.44.0 Depends: R (>= 4.0.0), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: 1ee43f8370a628a115e1c49ca37839c0 Package: GUIDEseq Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: d0e7e4a8e642370b1f07c4434ddd50dc Package: Guitar Version: 2.28.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 6c98151b774f442c67bf3ef8b037fb55 Package: gVenn Version: 1.1.1 Depends: R (>= 4.4.0) Imports: ComplexHeatmap, eulerr, GenomicRanges, IRanges, lubridate, methods, rtracklayer, stringr, writexl Suggests: testthat (>= 3.0.0), ggplot2, withr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e15bb7cd781e995f161b66dab0fe1ecf Package: Gviz Version: 1.56.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.61.1), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.69.1), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.61.4), ensembldb (>= 2.11.3), BSgenome (>= 1.77.1), Biostrings (>= 2.77.2), biovizBase (>= 1.13.8), Rsamtools (>= 2.25.1), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.45.1), Seqinfo, GenomeInfoDb, BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 1115c081bf88d6828390c12ae276465a Package: GWAS.BAYES Version: 1.22.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 89219d5c20ec33d70bd8a80e2233c94a Package: gwascat Version: 2.44.0 Depends: R (>= 4.1.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, Seqinfo, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub, data.table, tibble Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: e4af9977a3110a46f014907ca5415507 Package: GWASTools Version: 1.58.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, 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Package: HiCcompare Version: 1.34.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: 03373a1e42a1fce6757224e8258eaad2 Package: HiCDCPlus Version: 1.20.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: d28f67ce7250d9bfc4570a9ffd41ccd9 Package: HiCDOC Version: 1.14.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, Seqinfo LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: 5323a9a8e2e578979cf5c79040ba514b Package: HiCExperiment Version: 1.12.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d38cf3d12eb90ad999ef6648289e0559 Package: HiContacts Version: 1.14.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9ca434381f1d9a5af9cf8c7f74ae36b4 Package: HiCool Version: 1.12.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk.utils, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1675eb518b9f2e51e3d29060ae320d4e Package: HiCParser Version: 1.4.0 Imports: data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, Seqinfo LinkingTo: Rcpp Suggests: rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: 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BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 MD5sum: 18561ed5007ce49ee0a84111cbc665dd Package: hmdbQuery Version: 1.31.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 MD5sum: a2f3e34d557b19105df389fb17697da8 Package: HMMcopy Version: 1.54.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 MD5sum: 119e4311e924dc51a26c3b6053ab8538 Package: HoloFoodR Version: 1.6.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment Imports: dplyr, httr2, jsonlite, S4Vectors, stringi, stats, SummarizedExperiment, utils Suggests: BiocStyle, DT, ggh4x, ggsignif, knitr, MGnifyR, mia, miaViz, MOFA2, patchwork, reticulate, rmarkdown, scater, shadowtext, testthat, UpSetR License: Artistic-2.0 | file LICENSE MD5sum: 73e4c6e6be36f63c061b3247dd12798a Package: hoodscanR Version: 1.10.0 Depends: R (>= 4.3) Imports: knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: 49a116659641a89060ab7ca8fb4e3809 Package: hopach Version: 2.72.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: 71babce96afceac3708560076bf1c8dc Package: HPAanalyze Version: 1.30.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 2158dccf81bbab84ab89389c38884095 Package: hpar Version: 1.54.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: f159282d941e85a79d4b82eacf76ef0b Package: HPiP Version: 1.18.0 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: 8ba6bb654bf9cb60896469be4e5a9de9 Package: HTqPCR Version: 1.66.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: e787a90c7810a764ea64fe8db0df3343 Package: HTSFilter Version: 1.52.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e1b9e43520c258fb951b6e20470c1d31 Package: HuBMAPR Version: 1.6.2 Depends: R (>= 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LICENSE MD5sum: 72808b1ea489619512cd196fb75fc61e Package: HybridExpress Version: 1.8.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: c5681f84de9708a5725cb11dab25de08 Package: HybridMTest Version: 1.56.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: 86edda47d75591c26ec81fe153806380 Package: hypeR Version: 2.10.0 Depends: R (>= 3.6.0) Imports: ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny, BiocStyle Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 0309dcb5bc9a0ff0ee7b30fb63760463 Package: hyperdraw Version: 1.64.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, 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SingleCellExperiment, stats, SummarizedExperiment, tensorflow, tools Suggests: basilisk.utils, BiocStyle, bluster, dplyr, ggplot2, kableExtra, knitr, lifecycle, markdown, mumosa, patchwork, Peptides, rmarkdown, scater, spelling, testthat (>= 3.0.0), utils, viridis License: MIT + file LICENSE MD5sum: 873710a7f36000faeb8710f72960791a Package: ibh Version: 1.60.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: cd9badd70f80684d2f9c7b87ab17aeed Package: iCARE Version: 1.40.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE MD5sum: 34616b6f96b07e6e3f6bc930348a011e Package: Icens Version: 1.84.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: ac2e0dc1c327eb9be7b44d2bd5ce49e6 Package: icetea Version: 1.30.0 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: GenomeInfoDb, knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: f3ac4680eef9fcd390c9cb54b15f08d8 Package: iCheck Version: 1.42.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: a36f26de04bd4aea8065ca696cd17bf3 Package: iChip Version: 1.66.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 1ff1a11821531255760cfb33169b0d31 Package: iClusterPlus Version: 1.48.0 Depends: R (>= 4.1.0), irlba, parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: a6c6382c81ec5501baa2cbb904603805 Package: iCNV Version: 1.32.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 7605ef865d281f138b566f2add3056f7 Package: iCOBRA Version: 1.40.0 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, utils, rlang, prompter Suggests: knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 1ed5796526d10021d1fcab27745d06f8 Package: ideal Version: 2.6.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, graphics, base64enc, methods, utils, stats Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR License: MIT + file LICENSE MD5sum: e8a44ee5b15065828a0d2802a8e8060f Package: IdeoViz Version: 1.48.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: 06863421bd34e376e250add80da950b8 Package: idiogram Version: 1.88.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 06ddf45f01dc3eb869c72ec78a121d61 Package: idpr Version: 1.22.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: d9aa7cac86a4f474d68b4c486c296148 Package: idr2d Version: 1.26.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 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GenomicAlignments, parallel, testthat, knitr, rmarkdown, BiocStyle, ggplot2, dplyr, scales, ggseqlogo, airr License: Artistic-2.0 MD5sum: c311b9abae8796d685286b6fcccfb3ed Package: iGC Version: 1.42.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: f519e207f388073c8da50cabf0e12390 Package: IgGeneUsage Version: 1.26.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE MD5sum: 5e9a2c7d5f8b308af5f32e3b99e03fb9 Package: igvR Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: 4e7a05896113d616eeba54326e99cd83 Package: igvShiny Version: 1.8.3 Depends: R (>= 3.5.0), GenomicRanges, methods, shiny Imports: BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, utils Suggests: BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, testthat, shinytest2, VariantAnnotation License: MIT + file LICENSE MD5sum: f3bc6903a676d276b6580cf6881edf0f Package: IHW Version: 1.40.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 6a9a3aa1af97e08280129280c394fd76 Package: illuminaio Version: 0.54.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: b5dd80c5ee387ab78261708b6b6a16d8 Package: ILoReg Version: 1.22.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: fa08240bc1511938c611d1e7a8a12d68 Package: ImageArray Version: 1.0.0 Depends: R (>= 4.5.0), EBImage Imports: methods, grDevices, S4Arrays, S4Vectors, DelayedArray, rhdf5, HDF5Array, Rarr, ZarrArray, magick, tools Suggests: testthat (>= 3.0.0), knitr, ggplot2, shiny, RBioFormats, BiocFileCache, BiocStyle License: MIT + file LICENSE MD5sum: 74940587e60e03313efe0c523acece98 Package: imageFeatureTCGA Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocFileCache, BiocIO, BumpyMatrix, dplyr, httr2, IRanges, methods, readr, rjsoncons, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, TCGAutils, TENxIO, tibble, utils Suggests: AnnotationDbi, anndataR, BiocStyle, BiocParallel, cowplot, curatedTCGAData, curl, ggplot2, imageTCGAutils, knitr, png, RColorBrewer, rhdf5, rmarkdown, SpatialFeatureExperiment, tinytest, yaml License: Artistic-2.0 MD5sum: 75fed8badb3b70b2d8910748454180cc Package: imageTCGA Version: 1.4.0 Depends: R (>= 3.5.0), shiny Imports: DT, dplyr, bslib, bsicons, ggplot2, viridis, tidyr, leaflet, clipr, rlang Suggests: BiocManager, BiocStyle, knitr, curl, glue, rmarkdown, sessioninfo, testthat, tibble, GenomicDataCommons License: Artistic-2.0 MD5sum: f700475fc44a7a32588412e35dcd128d Package: imageTCGAutils Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, data.table, dplyr, grDevices, methods, rlang, S4Vectors, SpatialExperiment, SummarizedExperiment Suggests: anndataR, BiocStyle, imageFeatureTCGA, ggplot2, knitr, paws, rhdf5, rmarkdown, sfdep, spdep, SpatialFeatureExperiment, tinytest License: Artistic-2.0 MD5sum: e3e7e2f1017f4964f709e667d0380a53 Package: IMAS Version: 1.35.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, Seqinfo, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 MD5sum: 098a0d929b3f12d1d1bed180fada961b Package: imcRtools Version: 1.18.1 Depends: R (>= 4.1), SpatialExperiment Imports: S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scrapper, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: afe594cd5034c00fa1343fd674ae7a90 Package: IMMAN Version: 1.32.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: f0b45822a5cfbb04260b6fbb073509ef Package: immApex Version: 1.6.0 Depends: R (>= 4.3.0) Imports: immReferent, Matrix, matrixStats, methods, Rcpp, SingleCellExperiment, stats, stringr, utils LinkingTo: Rcpp Suggests: BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown, Peptides, randomForest, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis License: MIT + file LICENSE MD5sum: 431d9a3344b9a4237674d4aea340d5ae Package: immLynx Version: 1.0.0 Depends: R (>= 4.5.0) Imports: basilisk (>= 1.8.0), reticulate (>= 1.24), immApex, methods, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, ggplot2, knitr, markdown, rmarkdown, scater, scran, scRepertoire, spelling, testthat (>= 3.0.0), withr License: MIT + file LICENSE MD5sum: b5541c016fa5921e9ba9c2abb79bfcbb Package: immReferent Version: 1.0.0 Depends: R (>= 4.5.0) Imports: Biostrings, httr, jsonlite, methods, rvest, tibble, yaml Suggests: BiocManager, BiocStyle, knitr, mockery, spelling, rmarkdown, testthat (>= 3.0.0), withr License: MIT + file LICENSE MD5sum: 1db8c7d8e66bfeeedb271aea491176c2 Package: immunoClust Version: 1.44.0 Depends: R(>= 4.2), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 MD5sum: 8a5bb3b1f486c63d132e90605ff587ed Package: immunogenViewer Version: 1.6.0 Depends: R (>= 4.0) Imports: ggplot2, httr, jsonlite, patchwork, UniProt.ws Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT License: Apache License (>= 2) MD5sum: 960f259033107331c97c3287df6f26df Package: immunotation Version: 1.19.0 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 MD5sum: 3e0bd6e26957fcf0d8af85768c86007b Package: iModMix Version: 1.2.0 Depends: R (>= 4.5.0) Imports: config (>= 0.3.2), golem (>= 0.4.1), shiny (>= 1.7.5), ComplexHeatmap, DT, RColorBrewer, WGCNA, corrplot, cowplot, dynamicTreeCut, ggplot2, glassoFast, impute, purrr, stringr, tidyr, visNetwork, shinyBS, httr, dplyr, stats, iModMixData, SummarizedExperiment, ExperimentHub (>= 2.99.0) Suggests: testthat (>= 3.0.0), ggfortify, shinyWidgets, pROC, tuneR, knitr, curl, readxl, reshape2, vroom, here, enrichR, rmarkdown License: GPL-3 MD5sum: 1eaae2fe4b645da5efffd8f229d6ab02 Package: IMPCdata Version: 1.48.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: be17835dac6a2a47121e7fb49309ea8e Package: impute Version: 1.86.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: d0a5c043bf376586e5f8849966e80d66 Package: INDEED Version: 2.26.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: c0ceca39d6ffc9aed5398d0680823ece Package: iNETgrate Version: 1.10.0 Depends: R (>= 4.3.0), BiocStyle (>= 2.18.1) Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA, grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26), Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast, tidyr, tidyselect, utils Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) License: GPL-3 MD5sum: f59ff1ee66dbb7b8adbf8e6ac6934295 Package: infercnv Version: 1.28.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 2bfc4a93a1717ba9161e6f9e2b3e2e31 Package: infinityFlow Version: 1.22.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost (>= 3.0.0) Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: a2c089d291f82b3a3912658fbcad8269 Package: Informeasure Version: 1.22.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 4144cd683ec2d05a27589f70b3b38236 Package: InPAS Version: 2.20.0 Depends: R (>= 3.5) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, 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grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: bf0f3189139a468312202b3af8fd7e79 Package: IntramiRExploreR Version: 1.34.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 5cb5c2ae9d0b1a857cfab360c27b5bb6 Package: IONiseR Version: 2.35.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 63440027ebb7744f1ec17e5a7ff91013 Package: iPath Version: 1.18.0 Depends: R (>= 4.1), mclust, BiocParallel, survival Imports: Rcpp (>= 1.0.5), matrixStats, 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knitr, microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools, SummarizedExperiment, S4Vectors, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 132ae01fc6e7ef84e3bed792a025a57b Package: iSEE Version: 2.24.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2 (>= 3.4.0), ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: b1aff497d906e7800a6296a330d6a648 Package: iSEEde Version: 1.10.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, 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sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: 67fcf77d12adaa253d9f736fdfc38603 Package: iSEEindex Version: 1.10.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown, scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: 417cb80b98987c9ab1b17f00bff3a76d Package: iSEEpathways Version: 1.10.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: b43792d444e13171f9f5183d3b713fa0 Package: iSEEtree Version: 1.6.0 Depends: R (>= 4.4.0), iSEE (>= 2.19.4) Imports: ape, ggplot2, ggtree, grDevices, methods, miaViz, purrr, S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment, SummarizedExperiment, tidygraph, TreeSummarizedExperiment, utils Suggests: biomformat, BiocStyle, knitr, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan License: Artistic-2.0 MD5sum: 46c96a0b24b9ee57de210142b04a4352 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IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: d918567f3dd69b473a643e8a558ff4a9 Package: IsoCorrectoRGUI Version: 1.28.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: afb2f51bc5d8722a998e02e6d1547da8 Package: IsoformSwitchAnalyzeR Version: 2.12.0 Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, Seqinfo, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) MD5sum: 7f8ccb920151289652140a5f7b4ede41 Package: ISoLDE Version: 1.40.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: 89d6b16eadb7cedc9ded0c4d568ead24 Package: isomiRs Version: 1.40.0 Depends: R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: bdf62b68e6da370131a3f7717337104a Package: ITALICS Version: 2.72.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: 54a8cca23718a5688bddaa8d5398dab7 Package: iterativeBMA Version: 1.70.0 Depends: BMA, 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Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: XVector, knitr License: GPL (>= 2) MD5sum: 36993b3254500b504b381ba42932da76 Package: jazzPanda Version: 1.4.0 Depends: R (>= 4.5.0) Imports: spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr, doParallel, BiocParallel, methods, BumpyMatrix,SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod, corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2, igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr, SpatialFeatureExperiment, ExperimentHub, TENxXeniumData, SingleCellExperiment, SFEData, Matrix, data.table, scran, scater, grid, GenomeInfoDb, testthat (>= 3.0.0) License: GPL-3 MD5sum: cddbc9b0a050400ec1f67ab3856442ae Package: jvecfor Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocNeighbors, BiocParallel, Matrix, bluster, data.table, methods, processx Suggests: BiocStyle, 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methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 1fbaa812efc21355c3aef68873abbc4f Package: KEGGgraph Version: 1.72.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: 38c8f2c510a0a51a7e0429afbee43d06 Package: KEGGlincs Version: 1.38.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 887b1028f8b7f1a19e3b30a606d524a6 Package: keggorthology Version: 2.64.0 Depends: R (>= 2.5.0), hgu95av2.db, graph Imports: AnnotationDbi, DBI, grDevices, methods, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: c59a3b2663e34c2f82bbbe695c1d4461 Package: KEGGREST Version: 1.52.2 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 5dc0d6b7bd92a95d3ec76f143a80db90 Package: KinSwingR Version: 1.30.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 57d9a702b2ae7bec28bd041b31d989c2 Package: kissDE Version: 1.32.0 Imports: aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT, rlang Suggests: BiocStyle, quarto, testthat License: GPL (>= 2) MD5sum: 3aeefa64ca87a2e49e0a5c23960f5794 Package: kmcut Version: 1.6.0 Imports: survival, tools, methods, pracma, doParallel, foreach, parallel, SummarizedExperiment, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, License: Artistic-2.0 MD5sum: 6b3e0b156d131ab1d6dee6159b5536f4 Package: KnowSeq Version: 1.25.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: dc48b50c24517ed9b805444235adfd9a Package: knowYourCG Version: 1.8.0 Depends: R (>= 4.4.0) Imports: sesameData, ExperimentHub, AnnotationHub, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr, readr Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2, ggrastr License: AGPL-3 MD5sum: cff37643a45efb7eb5bdc3d596312cbf Package: koinar Version: 1.6.0 Depends: R (>= 4.3) Imports: httr, jsonlite, methods, utils Suggests: BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice, testthat, OrgMassSpecR, protViz, S4Vectors License: Apache License 2.0 MD5sum: 6bfd34dafdfa9e80426226797e4db911 Package: LACE Version: 2.16.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 582661a8e089e5fc629fca37782460b1 Package: LACHESIS Version: 1.0.0 Depends: R (>= 4.3) Imports: data.table, vcfR, tidyr, stats, utils, graphics, grDevices, ggplot2, gridExtra, survival, survminer, RColorBrewer, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown, knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges, MutationalPatterns, magick License: GPL (>= 3) MD5sum: 81d6e9aec737d5c9ef11c8ee2dfd33ca Package: LBE Version: 1.80.0 Depends: stats Imports: graphics, stats, utils Suggests: qvalue License: GPL-2 MD5sum: aee4f966bc548685b6f1cb9e08a7c93a Package: lcmsPlot Version: 1.0.0 Depends: R (>= 4.4.0) Imports: methods, rlang, dplyr, tibble, tidyr, BiocParallel, MSnbase, xcms, MsExperiment, mzR, Spectra, MsBackendMsp, S4Vectors, ggplot2, scales, patchwork, DBI, RSQLite Suggests: knitr, rmarkdown, BiocStyle, openxlsx, faahKO, rawrr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 60430a783f83a22d146ec4314e579337 Package: ldblock Version: 1.42.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), Seqinfo, httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: c92b840eda6d4696f336d60fc9290505 Package: LEA Version: 3.24.0 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: 490f4b428a188c7b3a8eef406d522910 Package: leapR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: stats, gplots, readr, tibble, gplots, methods, ggplot2, dplyr, stringr, tidyr, SummarizedExperiment, BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a9c424f113fae5d90af27442388a6ef1 Package: LedPred Version: 1.46.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: 337bc7f098dab4e43ad49cf2d778dd8f Package: lefser Version: 1.22.0 Depends: SummarizedExperiment, R (>= 4.5.0) Imports: coin, MASS, ggplot2 (>= 3.4.0), S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr License: Artistic-2.0 MD5sum: c15c37f4e5163cff16add77c68f6d5e9 Package: lemur Version: 1.10.2 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0), glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, quarto, BiocStyle License: MIT + file LICENSE MD5sum: b1ed5f663fc8b61eb77ba57a20f372e6 Package: les Version: 1.62.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: dd2ef725364722ff86e3f1918aef5307 Package: levi Version: 1.30.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 3687208ba52de5db14b929529448ba63 Package: lfa Version: 2.12.0 Depends: R (>= 4.0) Imports: methods, corpcor, RSpectra, BEDMatrix, genio Suggests: knitr, rmarkdown, ggplot2, testthat License: GPL (>= 3) MD5sum: c4221f9acd166c03565dd4e3d65d1b76 Package: Lheuristic Version: 1.4.0 Depends: R (>= 4.4.0) Imports: Hmisc, stats, energy, grDevices, graphics, utils, MultiAssayExperiment, ggplot2, ggpubr Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 486ce3194a77d98e1c317df03e7156a5 Package: limma Version: 3.68.5 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) MD5sum: c6811a1e4a2939ad306af72632eb31ad Package: limmaGUI Version: 1.88.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: 175afaa43646e9d5547c9bda8280d7de Package: limpa Version: 1.4.0 Depends: limma Imports: methods, stats, data.table, statmod Suggests: knitr, nanoparquet, BiocStyle License: GPL (>= 2) MD5sum: ac6725599fdd89303a846c3f6eed34f0 Package: limpca Version: 1.8.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: c8cc6168a19a97214df109c23fdabd38 Package: LimROTS Version: 1.4.0 Depends: R (>= 4.5.0), SummarizedExperiment Imports: limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors, dplyr, survival, cmprsk, variancePartition Suggests: BiocStyle, ggplot2, testthat (>= 3.0.0), knitr, rmarkdown, caret, ROTS, mia, miaTime, TreeSummarizedExperiment License: GPL (>= 2) MD5sum: a9983d00e4e7bcaca3888ab82130f72b Package: lineagespot Version: 1.16.1 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f66d8cd97599a3f3a93017107b781fc3 Package: LinkHD Version: 1.26.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 6a9419cd141aa51bbd7e61d81feb5e08 Package: linkSet Version: 1.2.0 Depends: GenomicRanges, S4Vectors, R (>= 4.5.0) Imports: methods, IRanges, GenomeInfoDb, BiocGenerics, Organism.dplyr, InteractionSet, ggplot2, patchwork, scales, foreach, iterators, stats, rlang, MASS, data.table, DBI, doParallel, AnnotationDbi Suggests: knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Hs.eg.db, GenomicFeatures, GenomicInteractions, gamlss, gamlss.tr, BiocStyle, rtracklayer License: MIT + file LICENSE MD5sum: 21d86355b6a58a27a47f082e467e70c8 Package: Linnorm Version: 2.36.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE MD5sum: 64d805955d183d09982fb75c1043a674 Package: lionessR Version: 1.26.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: b71a5be61791cfafff1df35c8ad489d3 Package: lipidr Version: 2.26.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 51589f3368e12272729c8bd2e7310c1a Package: LipidTrend Version: 1.2.0 Depends: R (>= 4.5.0) Imports: dplyr, ggnewscale, ggplot2, magrittr, methods, rlang, SummarizedExperiment, matrixTests Suggests: BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>= 3.0.0), S4Vectors, Enhances: data.table, License: MIT + file LICENSE MD5sum: e00ff381f9b388cded19ef8f27625733 Package: LiquidAssociation Version: 1.66.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 3eeccc153bbfeb3b2dc25fa6e08f0e76 Package: lisaClust Version: 1.20.0 Depends: R (>= 4.1.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random, lifecycle, simpleSeg, rlang, Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 3fa6385b7452dceeef468c0b8b8bf0df Package: lmdme Version: 1.54.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: aa89990b8da380feec92afa42e8fe354 Package: lncRna Version: 1.0.0 Imports: fmsb, ggplot2, grDevices, graphics, Hmisc, patchwork, plotly, Polychrome, tidyr, S4Vectors, scales, stats, stringr, GenomicRanges, utils Suggests: IRanges, methods, BiocStyle, gprofiler2, knitr, rmarkdown, rtracklayer, seqinr, testthat (>= 3.0.0), venn License: MIT + file LICENSE MD5sum: 9a827a162896aeb670ad587444cbfcac Package: LOBSTAHS Version: 1.38.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: f5af87263ca532de6b9622a8fcd57a67 Package: loci2path Version: 1.32.0 Depends: R (>= 3.5) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b66b8c68cb49af4357bc1d7522258998 Package: logicFS Version: 2.32.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: 73f5007b12d2d144699fef25a4d3f420 Package: LOLA Version: 1.42.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, XVector, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: 3b5be082b1fcdd1cd59ecc297a88d143 Package: looking4clusters Version: 1.2.0 Depends: R (>= 4.5.0) Imports: stats, utils, SummarizedExperiment, SingleCellExperiment, BiocBaseUtils, jsonlite Suggests: knitr, rmarkdown, Seurat, parallelDist, uwot, NMF, fpc, dendextend, cluster, Rtsne, scRNAseq, Matrix License: GPL-2 | GPL-3 MD5sum: df43c6c5e5560ebdb444d1d5223617e6 Package: LoomExperiment Version: 1.30.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: aa4636c8dde73223c26e860832481e36 Package: LPE Version: 1.86.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: ea4a015ea1ca37a8ef049dbaf9094024 Package: lpNet Version: 2.44.0 Depends: lpSolve, KEGGgraph License: 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lumi Version: 2.64.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: cf860a8838a96ee5422e6373a91cde53 Package: LymphoSeq Version: 1.40.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: e2c351650fc6353bf6a653202814a03d Package: M3C Version: 1.34.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: 1621863aaab45902916f34b935bcaa2a Package: M3Drop Version: 1.38.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: 88eb5459fef6b2536fa5700acd1e1fb9 Package: m6Aboost Version: 1.18.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: eaee5d42dacf25a104b362b58d5d5138 Package: Maaslin2 Version: 1.26.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: a6bd205eb4d430bf5923aa65a7461618 Package: maaslin3 Version: 1.4.0 Depends: R (>= 4.4) Imports: data.table, collapse, lmerTest, lme4, optparse, logging, mirai, multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang, ggnewscale, survival, methods, BiocGenerics, reformulas Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra, dplyr, SummarizedExperiment, TreeSummarizedExperiment License: MIT + file LICENSE MD5sum: 7825cbab7fdd9e290ec0c4494cd81a1e Package: Macarron Version: 1.16.0 Depends: R (>= 4.5.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: 0d28cd30578e6c00be35a823960c8abb Package: maCorrPlot Version: 1.82.0 Depends: lattice Imports: graphics, grDevices, 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IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 MD5sum: e86798d5d39f5d12ad5d50604393637f Package: MeasurementError.cor Version: 1.84.0 License: LGPL MD5sum: df7110e430e4c31e543ef304624994e7 Package: MEAT Version: 1.24.0 Depends: R (>= 4.0) Imports: impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0), grDevices, graphics, stats, utils, stringr, tibble, RPMM (>= 1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 66876a9d52ed6cc58baa27e270ee8a76 Package: MEB Version: 1.26.0 Depends: R (>= 3.6.0) Imports: e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment Suggests: knitr,rmarkdown,BiocStyle License: GPL-2 MD5sum: acc3cfcb24d903255c80c75ac5e35a0a Package: MEDIPS Version: 1.64.0 Depends: R (>= 3.0), BSgenome, Rsamtools 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forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: 2bef2d82a7df69e3c6d79076a4ee7744 Package: Mergeomics Version: 1.40.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: db90f5660f02602fba64581ca8aad26c Package: MeSHDbi Version: 1.48.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: e4153dc72d2439bb4649bfc7a74a2b65 Package: meshes Version: 1.38.0 Depends: R (>= 4.1.0) Imports: enrichit, gson, AnnotationDbi, GOSemSim (> 2.37.0), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 945c27ef5df4c7d133e3441f2eaddadc Package: meshr Version: 2.18.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: 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(>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: bf1447832c3ea0ee6244eb339b33ff45 Package: metabinR Version: 2.0.0 Depends: R (>= 4.4), methods Imports: BiocGenerics, BiocParallel, Biostrings, checkmate, cli, rJava, S4Vectors, ShortRead, utils Suggests: BiocStyle, covr, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6908d0f59f2af3373100bcfe78629e82 Package: MetaboAnnotation Version: 1.16.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.21.5), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, MsDataHub, BiocStyle, rmarkdown, plotly, shiny, shinyjs, msentropy, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 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(>= 4.4) Imports: broom, ComplexUpset (>= 1.3.3), cosmosR, DBI, dplyr, EnhancedVolcano, factoextra, ggbeeswarm, ggfortify, ggplot2 (>= 3.3.5), ggpubr, ggrepel, grid, gridExtra, gtools, hash, igraph, ggraph, inflection, limma, logger, magrittr, methods, OmnipathR (>= 3.19.12), patchwork, pheatmap, Polychrome, purrr, qcc, qvalue, rappdirs, readr, rlang, rstatix, S4Vectors, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, writexl Suggests: BiocStyle, ggupset, ggVennDiagram, kableExtra, knitr, pkgdown, svglite, testthat (>= 3.1.4) License: BSD_3_clause + file LICENSE MD5sum: 7f63fed6bb566836d29838b5f1b0bd3d Package: metaSeq Version: 1.52.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: a4bc2ab1d5cf717b28e01d513fc42c4a Package: metaseqR2 Version: 1.24.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 3fa6f8fb604d140121ed8cc21d055a58 Package: MetCirc Version: 1.42.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 01fea97abaf897c184c32b21c6c79c5f Package: methimpute Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 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Suggests: rmarkdown License: GPL (>= 3) MD5sum: 38017549eb36ec329bb908b26224ced3 Package: MethPed Version: 1.40.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 7b6a71b7f73573805143a4cbcd2e9bfe Package: MethReg Version: 1.21.1 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader License: GPL-3 MD5sum: f217bf345850a6cbcaa86c43b5e27860 Package: methrix Version: 1.26.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: e0c4dd79cd3c27ac0ce9ca6cab85c99e Package: MethTargetedNGS Version: 1.44.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: 69b9576af97280d6b8a1b138506d420a Package: MethylAid Version: 1.46.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 269f8d8eaacc7527db8143cde21acfb8 Package: methylCC Version: 1.26.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: c86be84d2c9785ffd3ef2398b5f1ceae Package: methylclock Version: 1.18.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: 7900bfc1b7939ef2847cc80ab2ad63b1 Package: methylGSA Version: 1.30.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 9b2088f85e86fdd28896cb4d9dd4a24f Package: methyLImp2 Version: 1.8.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: fcb2b650459df4f3f7cefa4cd7baac41 Package: methylInheritance Version: 1.36.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3e3058ed5d38a17f348ed467f404f0a4 Package: methylKit Version: 1.38.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: 3c3e2bfa3cf46d3a51fe8014dfdd4ee5 Package: MethylMix Version: 2.42.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 0c5c9181f9d959628c8720e8ad6f5f37 Package: methylMnM Version: 1.50.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 2763d97ab33f69a8fd3604c76d495113 Package: methylPipe Version: 1.46.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, Seqinfo, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: f7143856b6fa08c9e7ecc378f4a5d82b Package: methylscaper Version: 1.20.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: c98bccc46b13bca4ac3b1fe721c926cb Package: MethylSeekR Version: 1.52.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2), GenomeInfoDb Suggests: BSgenome.Hsapiens.UCSC.hg38 License: GPL (>= 2) MD5sum: 4e4bc0063b1455d44a21a8cf69a9696f Package: methylSig Version: 1.24.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: c153c686e0c6d87d0f1b6ecda27ef180 Package: methylumi Version: 2.58.1 Depends: Biobase, methods, R (>= 4.0), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, grDevices, stats, utils, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures, BiocParallel Suggests: lumi, limma, SQN, MASS, rtracklayer, Biostrings, quarto, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, testthat (>= 3.0.0) License: GPL-2 MD5sum: 657011fe86105d5527c4437fa70b2dab Package: MetID Version: 1.30.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 5968390d033af5ad81a0189c1125fc1e Package: MetMashR Version: 1.6.0 Depends: R (>= 4.3.0), struct Imports: dplyr, methods, httr, scales, ggthemes, utils, rlang, stats, ggplot2 Suggests: covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx, ggplotify, cowplot License: GPL-3 MD5sum: 736d0d63455ea8820c79cc721ade4f3d Package: MetNet Version: 1.30.0 Depends: R (>= 4.1), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 4.1), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: ab28b325b994965938125b4e5f29c1cf Package: Mfuzz Version: 2.72.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 6a928abe0f3c689dbc4fb378c0164b45 Package: MGFM Version: 1.46.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: f42bb513ea7011c723643145ba154cd7 Package: MGFR Version: 1.38.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: d2a5c77e5090328653d32edbdfd9b3b3 Package: MGnifyR Version: 1.8.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: b044b6a3407093d54becc0156cb4e478 Package: mgsa Version: 1.60.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 8fe314e5a0c5691298c3c884a5e4a1d1 Package: mia Version: 1.20.0 Depends: R (>= 4.1.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, methods, ecodive, rlang, S4Vectors, scater, stats, stringr, tibble, tidyr, utils, vegan, Rcpp LinkingTo: Rcpp Suggests: ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaTime, miaViz, microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist, rhdf5, rmarkdown, scuttle, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: c26efa1398d92bac9ffb8e9ed2b3b8e6 Package: miaDash Version: 1.4.0 Depends: R (>= 4.4.0), iSEE (>= 2.19.4), shiny Imports: ape, bluster, htmltools, iSEEtree (>= 1.1.4), mia, rintrojs, scater, scuttle, shinydashboard, shinyjs, shinyWidgets, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils, vegan Suggests: BiocStyle, knitr, philr, remotes, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cc45940322a82554fb63336155b57bdd Package: miaSim Version: 1.18.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 25d8c0f5818eba7810476f44bab58026 Package: miaTime Version: 1.2.0 Depends: R (>= 4.5.0), mia Imports: dplyr, methods, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, TreeSummarizedExperiment Suggests: BiocStyle, devtools, ggplot2, knitr, lubridate, miaViz, rmarkdown, scater, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: a231a879a240e8c0b4b869461824ec58 Package: miaViz Version: 1.20.0 Depends: R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports: ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, methods, patchwork, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor License: Artistic-2.0 | file LICENSE MD5sum: cd1bb0b4002b6ae9fa546fcb47d66943 Package: MiChip Version: 1.66.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 3e4e22b18fbf37c3bbfbb7ebef43aca4 Package: microbiome Version: 1.34.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 25502905f9b2049e27570195b4b6189e Package: microbiomeDASim Version: 1.26.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 467f110974baa911450ef5f3e3531eba Package: microbiomeExplorer Version: 1.22.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 7c7dfd9d1f56cf7d8df587938340f78c Package: MicrobiomeProfiler Version: 1.18.1 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), enrichit, config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 34805b3260c42e78e871b2d76e317cd5 Package: MicrobiotaProcess Version: 1.24.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager, rhdf5 License: GPL (>= 3.0) MD5sum: 9b0a6e078f44e0a2423a49ba119e207a Package: microRNA Version: 1.70.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: e3544762f7039353c052f7bcb15d84f3 Package: MICSQTL Version: 1.10.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: 4397a0898d04baf868646c04ff812f81 Package: midasHLA Version: 1.20.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 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rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 41ee74f92c7c5c203fc8b5568408f0b5 Package: mina Version: 1.20.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: 9a2e947427390ac988b80acc0ae05503 Package: minet Version: 3.70.0 Imports: infotheo License: Artistic-2.0 MD5sum: 7a58c627fabbaf9b8af2ee91ed490f4a Package: minfi Version: 1.58.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), bumphunter (>= 1.1.9) Imports: S4Vectors, Seqinfo, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 4ddcf3480a27542d12af2e7c42b34c93 Package: MinimumDistance Version: 1.56.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: a811c8e1cce77ef3ee063377c374495d Package: MiPP Version: 1.84.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: e9df87fa561e0c15dbd4c29a50438d62 Package: miQC Version: 1.20.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 87565a7420f2280dc4f57f18e1609d7f Package: MIRA Version: 1.34.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: fadc7f6b9143aea8b962cb468e82953a Package: MiRaGE Version: 1.54.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 9d92eb34e69c271320458a8cc58f6929 Package: miRBaseConverter Version: 1.36.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 0195f95a624e92610e765c6c791212d4 Package: miRcomp Version: 1.42.0 Depends: R (>= 3.5.0), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 9b703bf30610c2828087769a6f993f19 Package: mirIntegrator Version: 1.42.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 624fc27261733e82dbb9092f4d16fa14 Package: MIRit Version: 1.8.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: bb11deec452cc93ddf3a42d314f3b33a Package: miRLAB Version: 1.42.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 1aa4a0aaf9efe4fe5c2b2759e2d5ec22 Package: miRNAmeConverter Version: 1.40.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1f964950ba9c570a8824ddeb465b25f6 Package: miRNApath Version: 1.72.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 965047cdd0050265176587f6d7ae1caa Package: miRNAtap Version: 1.46.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 29c9b21698fba462ee3a67b63d2d2621 Package: miRSM Version: 2.8.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, BicARE, isa2, methods, rJava, Biobase, PMA, stats, dbscan, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 787e7fe41ebf87240a939d6086bed081 Package: miRspongeR Version: 2.16.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, utils, Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 1865d932d41a64f891e74e5b95c6a3ca Package: mirTarRnaSeq Version: 1.20.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 4536ea24f31561ef9d519ebef8d74592 Package: missMethyl Version: 1.46.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 6222e201600a5cd8f52f576c1378be3e Package: missRows Version: 1.32.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: fab9c5a19add7cc4ec63283f31694c74 Package: mist Version: 1.4.0 Depends: R (>= 4.5.0) Imports: BiocParallel, MCMCpack, Matrix, S4Vectors, methods, rtracklayer, car, mvtnorm, SummarizedExperiment, SingleCellExperiment, BiocGenerics, stats, rlang Suggests: knitr, rmarkdown, RUnit, ggplot2, BiocStyle License: MIT + file LICENSE MD5sum: 8aed73cba05b08772c8006aa2f32cbc1 Package: mistyR Version: 1.20.0 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost License: GPL-3 MD5sum: 7e390d593c6017c63d206164e32766d5 Package: mitch Version: 1.24.0 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra, dplyr, network Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: a71e1744dd9f8fac113984698d7c63c1 Package: mitoClone2 Version: 1.18.0 Depends: R (>= 4.4.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 59fa25314b9fb04ce5d909b7f83f4dfc Package: mitology Version: 1.4.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap, ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales Suggests: Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr, SummarizedExperiment, testthat License: AGPL-3 MD5sum: 81718349f0d632840c15ab13654e5d82 Package: mixOmics Version: 6.36.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, rgl, rlang Suggests: BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark, magick, vdiffr, kableExtra, devtools License: GPL (>= 2) MD5sum: ec9c607a8052fca6e7bd1aa1b35dbf48 Package: MLInterfaces Version: 1.92.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat, airway Enhances: parallel License: LGPL MD5sum: 7aeb19bf64036159317f9aeb04f84d87 Package: MLP Version: 1.60.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 2a2641feff3cfee15cbdea3d31d3c225 Package: MLSeq Version: 2.30.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 2e293aac3018494bbf7cf4d40324e6b4 Package: MMDiff2 Version: 1.40.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 5c7e66e494a5ce6ae21b50151a3172e3 Package: MMUPHin Version: 2.0.0 Depends: R (>= 3.6) Imports: maaslin3, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: f1976287027b2f48d0e50118aad787a6 Package: mnem Version: 1.28.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: 8faa8a00d2f2f126a11bdca8bf4702b5 Package: moanin Version: 1.19.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: bd048d89e2b2e04d8989b39618a6a96e Package: mobileRNA Version: 1.8.0 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 60b5c435d0ab58799a25a4633135f462 Package: MODA Version: 1.38.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: e612afac509278e85d80d02590b291b7 Package: ModCon Version: 1.20.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: 69fa983f4189b335ff10267c3303b631 Package: Modstrings Version: 1.28.0 Depends: R (>= 3.6), Biostrings (>= 2.79.3) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 9b4159dff840a24d037ea385547eeed4 Package: MOFA2 Version: 1.22.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: 344dc985c6e68fe278f6d1f8957aafab Package: MOGAMUN Version: 1.22.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: d7e11b74a8e6245781454eb6237690d3 Package: mogsa Version: 1.46.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 93bec8eecb7dd18d38b686423506bd9b Package: MoleculeExperiment Version: 1.12.0 Depends: R (>= 4.1.0) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d83a3858c3392ae87e83cb12f659be30 Package: MOMA Version: 1.24.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: aa08735b320994a14067fab2d4f452cd Package: monaLisa Version: 1.18.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: ffa2483b63f39d22e98ebfeddd349790 Package: monocle Version: 2.40.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 70b2ce59faff9b94ca0f84d794a19939 Package: Moonlight2R Version: 1.10.1 Depends: R (>= 4.5), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub, rlang, withr, data.table, fgsea Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: 3978966ece9a36c6c1a5dc3e18d57b6f Package: MoonlightR Version: 1.38.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: 5e621aa58d07c3ec35bbb7aa7e17402e Package: mosaics Version: 2.50.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 60fb9e25717e5a3ea3a6b7bc1726f976 Package: mosbi Version: 1.17.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: de125e3a4df83ad94605c71a5dd6f7f2 Package: MOSClip Version: 1.6.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 13dcfd360f07b95c9ad31bfe65e1fb1d Package: mosdef Version: 1.8.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: 6aa326489006fc60689f0ca314e6c4db Package: MOSim Version: 2.8.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: c2d318797c7da7b74abb22d646afcfa7 Package: Motif2Site Version: 1.16.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: 1d314d327c3ac7fbf1c1f17a8cca8888 Package: MotifDb Version: 1.54.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: ffd46bfe7fd2f0d11b6fa3e80665ea04 Package: motifmatchr Version: 1.34.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 5cbae7f693ef6219682b1af95c0623d1 Package: MotifPeeker Version: 1.4.0 Depends: R (>= 4.5.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat 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tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 408d2ff02428da82d621e4cf565c77ea Package: MsBackendMassbank Version: 1.20.0 Depends: R (>= 4.0), Spectra (>= 1.21.5) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: ba541d897803188ae8a36cc916b75892 Package: MsBackendMetaboLights Version: 1.6.1 Depends: R (>= 4.2.0), Spectra (>= 1.15.12) Imports: curl, ProtGenerics, BiocFileCache, S4Vectors, methods, progress, utils, MsCoreUtils (>= 1.23.8) Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: a26f3cb1acd91ad0275fdcbef93d3036 Package: MsBackendMgf Version: 1.20.1 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, 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S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, stringi, fastmatch, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, MsDataHub, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: 8b5b6d2dd9e687ab3b1112b32dc9120c Package: MsCoreUtils Version: 1.24.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest, rlang Enhances: HDF5Array License: Artistic-2.0 MD5sum: 5205d398fe42c77269232ba3f9f8c9f3 Package: MsDataHub Version: 1.12.1 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: 21a4594f395de5366b1ce6fc37a63277 Package: MsExperiment Version: 1.14.0 Depends: R (>= 4.2), ProtGenerics (>= 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Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: c01696e297a77b07041764dd1835dde5 Package: msqrob2 Version: 1.20.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools, matrixStats, ggplot2, assertthat, dplyr, grDevices, utils, rlang Suggests: stringr, ExploreModelMatrix, kableExtra, ComplexHeatmap, scater, multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, tidyr, plotly, MsDataHub, MSnbase, MsCoreUtils, covr, arrow, data.table, ggcorrplot, iq License: Artistic-2.0 MD5sum: ffb7de8742114e056503e4faaa1b4ad6 Package: MsQuality Version: 1.12.0 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), Chromatograms (>= 1.1.5), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), MsDataHub (>= 1.10.0), MsExperiment (>= 0.99.0), 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Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats, plotly, htmltools LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight License: Artistic-2.0 MD5sum: 23e95b2a2ad88994f318f93b40bf548c Package: MSstatsLOBD Version: 1.20.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: 873cdd54d67dab9c274cec3ef64fa57c Package: MSstatsPTM Version: 2.14.0 Depends: R (>= 4.3) Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert (>= 1.19.1), MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools, rlang LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr, mockery, arrow, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: c04a131e2289e6be8fc87f10377103ad Package: MSstatsQC Version: 2.30.0 Depends: R (>= 3.5.0) Imports: dplyr,plyr, plotly, 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utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet, shinydashboard, arrow, tools, MSstatsResponse, stringr, httr Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, License: Artistic-2.0 MD5sum: 85f52d60eb204d15e716c7ff22721d82 Package: MSstatsTMT Version: 2.20.0 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: ea793927dda5f3d84e4e8c40455c04c6 Package: MuData Version: 1.16.0 Depends: Matrix, S4Vectors, rhdf5 (>= 2.45) Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray, S4Vectors Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 MD5sum: 501c49d2c957f21569dfac33e436bec6 Package: Mulcom Version: 1.62.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 222a5fe5ab8d8ea9291ee261194ee4a1 Package: MultiAssayExperiment Version: 1.38.0 Depends: SummarizedExperiment, R (>= 4.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, h5mread, knitr, maftools, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: 6ff8b4dbebd558e46877c54aee774a6a Package: MultiBaC Version: 1.22.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: bcc6e1cfc887ba444ea1b80479ba2c65 Package: multiClust Version: 1.42.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 9c2443776f4eb591ec9d5afaf0880058 Package: multicrispr Version: 1.22.0 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, GenomeInfoDb, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 71c1843df8659e7719851cfef8c931fb Package: MultiDataSet Version: 1.40.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 1b2586d3cf53ea05743a9b0a0d124767 Package: multiGSEA Version: 1.22.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: 1025bd3578b4d32be1b1ded856996943 Package: multiHiCcompare Version: 1.30.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: cb62554a12271d9c4b5464cdc7e91646 Package: MultiMed Version: 2.34.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 72784ced6124d03397f6188f689e2322 Package: multiMiR Version: 1.34.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: 43f29a0b019bed86929cfa77cdd6565b Package: MultimodalExperiment Version: 1.12.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: df4eae8458073a2ac3de659511b6e623 Package: MultiRNAflow Version: 1.10.0 Depends: Mfuzz (>= 2.64.0), R (>= 4.4) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.20.0), DESeq2 (>= 1.44.0), factoextra (>= 1.0.7), FactoMineR (>= 2.11), ggalluvial (>= 0.12.5), ggplot2 (>= 3.5.1), ggplotify (>= 0.1.2), ggrepel (>= 0.9.5), gprofiler2 (>= 0.2.3), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4.1), plot3Drgl (>= 1.0.4), reshape2 (>= 1.4.4), rlang (>= 1.1.6), S4Vectors (>= 0.42.0), stats (>= 4.2.2), SummarizedExperiment (>= 1.34.0), UpSetR (>= 1.4.0), utils (>= 4.2.2) Suggests: BiocGenerics (>= 0.40.0), BiocStyle (>= 2.32.1), e1071 (>= 1.7.12), knitr (>= 1.47), rmarkdown (>= 2.27), testthat (>= 3.0.0) License: GPL-3 | file LICENSE MD5sum: ceffeef07dad4292713199303a05122d Package: multiscan Version: 1.72.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: c5283e165e263e4bb96df97a08265523 Package: multistateQTL Version: 2.4.0 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, collapse Imports: methods, S4Vectors, data.table, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: c3557f917dc3b3c3f44f4b0aa8c0f23c Package: multiWGCNA Version: 1.10.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, magrittr, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment, ggraph, tidyr Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 10802c812a6bc538138fb5b16cf1043c Package: multtest Version: 2.68.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: e9d6cb33f3697ced057bc930f3a35963 Package: mumosa Version: 1.20.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: d8c833dd7ff4a1a9e17066f647cb5c53 Package: MungeSumstats Version: 1.19.5 Depends: R(>= 4.1) Imports: data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, IRanges, ieugwasr(>= 1.0.1), BSgenome, Biostrings, stringr, VariantAnnotation, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: d1bf888d5e87d15280a4e20c621cb23a Package: muscat Version: 1.26.0 Depends: R (>= 4.5) Imports: BiocParallel, blme, ComplexHeatmap, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, MatrixGenerics, matrixStats, methods, progress, rlang, S4Vectors, scales, scater, scuttle, stats, SingleCellExperiment, SummarizedExperiment, variancePartition Suggests: BiocStyle, countsimQC, DESeq2, AnnotationHub, ExperimentHub, iCOBRA, IHW, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, sctransform, statmod, stageR, testthat, tidyr, UpSetR License: GPL-3 MD5sum: 0323c9edac02b5a318f34ae45f8a8c50 Package: muscle Version: 3.54.0 Depends: Biostrings License: Unlimited MD5sum: d11de2376fd034aa50198308208e7e3d Package: musicatk Version: 2.6.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 199b3f4b842bff1c3b935d48f08b11e6 Package: mutscan Version: 1.2.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp, edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally, ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw, rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray, tools LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager License: MIT + file LICENSE MD5sum: 4397674b07439930f510d2c9fa8cc1f9 Package: MutSeqR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, Biostrings, BSgenome, data.table, dplyr, GenomicRanges, ggplot2, here, IRanges, ggdendro, magrittr, methods, plyranges, rlang, S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, VariantAnnotation Suggests: binom, BiocManager, BiocStyle, bs4Dash, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, car, colorspace, dendsort, doBy, DT, ExperimentHub, fmsb, fs, ggrepel, gtools, htmltools, httr, knitr, lme4, magick, MutSeqRData, openxlsx, packcircles, patchwork, RColorBrewer, reticulate, rmarkdown, scales, shiny, testthat (>= 3.0.0), trackViewer, withr, yaml, xml2 License: MIT + file LICENSE MD5sum: 1c00c2c552fd2ab7b6fccb5c8650c0e9 Package: MVCClass Version: 1.86.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: a3f447e8df9c6243c8d1e6edb54bb1bb Package: MWASTools Version: 1.36.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 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knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: daf26973cf17d3355fb6a7cc5dd5cddc Package: NADfinder Version: 1.36.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: d80641df379e1882a41fd830b5cffdcf Package: NanoMethViz Version: 3.8.0 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr LinkingTo: Rcpp Suggests: BiocStyle, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: acb35a411b3c52fdd52735d5c6dd89ac Package: NanoStringDiff Version: 1.42.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 46522aa87e3a2ba7511b0865524a681b Package: NanoStringNCTools Version: 1.20.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: 5513b118be23cf2d95c904f57fe6d83e Package: NanoTube Version: 1.18.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE MD5sum: 8fd02f6523a319e5b9ea42751043eb85 Package: NBAMSeq Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: cefac3cebf804de7bd00c1eef0b2b2b0 Package: ncdfFlow Version: 2.58.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 9bfa3c0cef4780939f28361a73969817 Package: ncGTW Version: 1.26.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: a7d3bb7eab3517c32c61379627cf4c55 Package: NCIgraph Version: 1.60.0 Depends: R (>= 4.0.0) Imports: graph, KEGGgraph, methods, RBGL, RCy3, R.oo Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 7e5651177f15ffe66b431272af416c76 Package: ncRNAtools Version: 1.22.2 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: 0418194c20b0c4cd5ffe79e72e0a120d Package: ndexr Version: 1.34.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 675fa05e72bbce1ef4ba5c22c8ecb91e Package: Nebulosa Version: 1.22.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: 3ab7b00c9884f88849986a1ed1ff69a8 Package: nempi Version: 1.20.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: bdfc0b7e9a268eeb02da3b8787020dc6 Package: NetActivity Version: 1.14.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: ec1e4ca796e92b6dc78f8300cae73d83 Package: netboost Version: 2.20.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 OS_type: unix MD5sum: bdddefebbe283ac03ed80a763fa0939a Package: nethet Version: 1.44.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 4e76e1f66ca91419a2851da68cec6859 Package: NetPathMiner Version: 1.48.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: acae1e3b049bdb7db499d60b581e1392 Package: netprioR Version: 1.37.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 81da08e51fe5a3f22d4b8025dbaadba3 Package: netresponse Version: 1.72.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: bbb8a3d69146c29395b4f689e03a6bd3 Package: NetSAM Version: 1.52.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: 8d2e73149bcbbaee604640b0dca75e85 Package: netSmooth Version: 1.32.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: 9817e5b7a00b16815dc0b8879da9b94c Package: NewWave Version: 1.22.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 547ea57a9dd1c58ebdd1185cade2026a Package: ngsReports Version: 2.14.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: dcfab7928f6130d8469093de101a0d72 Package: nipalsMCIA Version: 1.10.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5acb88290adb130fba3d7551feb932b7 Package: nnNorm Version: 2.76.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 980fdb4a485930d9b27db9e9589f27df Package: nnSVG Version: 1.16.1 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 3e1441316db6a245a637627debce78b2 Package: NOISeq Version: 2.56.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 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org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, markdown License: MIT + file LICENSE MD5sum: 6b1293a7601fa0bb3abac8bf31e4deb4 Package: normalize450K Version: 1.40.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: dd7f6e9b2d088c8b4c74ac3b87df0fd3 Package: NormalyzerDE Version: 1.30.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 4037292147af5d283e50a893ff6f9bd6 Package: NormqPCR Version: 1.58.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 257ea670133d4288b4a75f26a69c7e78 Package: normr Version: 1.38.1 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: b3b3dd16539d937da0b58ea638aecb8d Package: notame Version: 1.2.0 Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment Imports: BiocGenerics, BiocParallel, dplyr, futile.logger, methods, openxlsx, S4Vectors, scales, stringr, tidyr, utils Suggests: BiocStyle, fpc, igraph, knitr, missForest, notameViz, notameStats, pcaMethods, RUVSeq, testthat License: MIT + file LICENSE MD5sum: 113759461e49267f131625a120ae250a Package: notameStats Version: 1.2.0 Depends: R (>= 4.5.0), SummarizedExperiment, Imports: BiocGenerics, BiocParallel, broom, dplyr, methods, notame, stats, tibble, tidyr, utils Suggests: BiocStyle, car, knitr, lmerTest, missForest, mixOmics, MuMIn, MUVR2, notameViz, PERMANOVA, PK, randomForest, rmcorr, testthat License: MIT + file LICENSE MD5sum: 82324da61c75cb35fd224df0c5bb75b1 Package: notameViz Version: 1.2.0 Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment Imports: BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro, ggrepel, grDevices, limma, methods, notame, pcaMethods, qpdf, Rtsne, scales, stringr, stats, tibble, tidyr, utils Suggests: batchCorr, BiocStyle, igraph, knitr, notameStats, testthat License: MIT + file LICENSE MD5sum: 3aacc4f6690092d8d9e62342f16f5c3a Package: NPARC Version: 1.24.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: d87d49146e010c71c1e8f67436b2b578 Package: npGSEA Version: 1.48.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: e040157d3f390afe4c1be66e7a2cc1d4 Package: NTW Version: 1.62.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: d89b1d1b36811c9a66f4553a8b63446c Package: nucleoSim Version: 1.40.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 02768b7095ab0f87cdd06284a442596a Package: nucleR Version: 2.44.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, Seqinfo, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 4e42ec188f1ee842660dbdc28c4d0cde Package: nuCpos Version: 1.30.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: c054b4f50b7a6d6eb4e68b9fbf14198b Package: nullranges Version: 1.18.0 Depends: R (>= 4.2.0) Imports: stats, IRanges, GenomicRanges, Seqinfo, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, GenomeInfoDb, nullrangesData, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, magrittr, tidyr, cobalt, DiagrammeR, MatchIt, mariner License: GPL-3 MD5sum: 43b944b2571eb1fb5986eed717c65884 Package: NuPoP Version: 2.20.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 014b0b0499dbc376933072c91e691d33 Package: OAtools Version: 1.0.0 Depends: R (>= 4.5) Imports: basilisk (>= 1.20.0), Biobase (>= 2.70.0), dplyr (>= 1.1.4), DT (>= 0.34.0), ggplot2 (>= 3.5.2), janitor (>= 2.2.1), methods (>= 4.5.2), plotly (>= 4.11.0), purrr (>= 1.2.0), ReadqPCR (>= 1.56.0), readxl (>= 1.4.5), reticulate (>= 1.43.0), rlang (>= 1.1.6), rmarkdown (>= 2.29), S4Vectors (>= 0.48.0), shiny (>= 1.13.0), SummarizedExperiment (>= 1.40.0), tibble (>= 3.3.0), tidyr (>= 1.3.1), writexl (>= 1.5.4) Suggests: testthat (>= 3.0.0), knitr, kableExtra (>= 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Package: OGRE Version: 1.16.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, Seqinfo, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 MD5sum: 1f23ba392399bb53a288095e97fef6c8 Package: oligo Version: 1.76.0 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, bit LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: e4e3b5e8de086859fcc9a81e70f139f7 Package: oligoClasses Version: 1.74.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 51e98a40748e715d51a6517a6319790c Package: OLIN Version: 1.90.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 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MD5sum: 70cef2ddaaa0154d00e130c3e50a5d24 Package: OmicCircos Version: 1.50.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 0e5d31946027482f00354484b727cc75 Package: omicplotR Version: 1.32.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: d259dfebb35655862af2c57aeb743d63 Package: omicRexposome Version: 1.34.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: f106fae8a135f5351e8a66647b8c0c7d Package: omicsGMF Version: 1.2.0 Depends: R (>= 4.5.0), sgdGMF, SingleCellExperiment, scuttle, scater Imports: stats, utils, Matrix, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, BiocSingular, BiocParallel, beachmat, ggplot2, methods, QFeatures Suggests: knitr, dplyr, testthat, BiocGenerics, BiocStyle, graphics, grDevices License: Artistic-2.0 MD5sum: 2b3d35edbc8aa697a1f74995d5d72125 Package: OmicsMLRepoR Version: 1.6.0 Depends: R (>= 4.4.0) Imports: dplyr, stringr, rols, tidyr, methods, stats, tibble, data.tree, jsonlite, plyr, BiocFileCache, readr, DiagrammeR, rlang, lubridate Suggests: arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>= 3.0.0), cBioPortalData License: Artistic-2.0 MD5sum: fe0ef3c703c17d2f0c29cf5019aeec1e Package: OMICsPCA Version: 1.30.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, Seqinfo, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 4c8a3e5f202c4c3db3a25df5be1253a3 Package: omicsPrint Version: 1.32.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: de5e7fd88fe696df7f775456b767beda Package: omicsViewer Version: 1.16.0 Depends: R (>= 4.2) Imports: htmltools, shinydashboard, survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: 9f221087f697ae494a517893e0a2d402 Package: Omixer Version: 1.22.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: a79ead663eabe070e18d842a4a88d0e6 Package: OmnipathR Version: 3.19.2 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), fs, httr2, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof, testthat License: MIT + file LICENSE MD5sum: 3c10df6d1d6b090d6499026dfd7ff5de Package: ompBAM Version: 1.16.0 Imports: utils, Rcpp Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a913226ad57672191be050f65bcef085 Package: omXplore Version: 1.6.0 Depends: R (>= 4.5.0), methods Imports: DT, shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, plotly, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals, Biobase Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: 341e7372786149c4b3cd80d74ce304a4 Package: oncomix Version: 1.34.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 5f9953f9303d9eebc7fd74751eaea380 Package: oncoscanR Version: 1.14.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 12e5fbfbd90a8e89ba1bad54397aba3b Package: OncoScore Version: 1.40.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 0cc9f84388897f08ac0a63d91974df1d Package: OncoSimulR Version: 4.14.0 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 81956a97749a49b6b50541b35d7e20a1 Package: onlineFDR Version: 2.20.0 Imports: stats, Rcpp, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: ab9aa228415152a3b89656861e56d6d2 Package: ontoProc Version: 2.6.0 Depends: R (>= 4.1), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk, jsonlite, RBGL, ellmer Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick, License: Artistic-2.0 MD5sum: f99d3bec965ff64654b40246cf5007e5 Package: openCyto Version: 2.24.0 Depends: R (>= 3.5.0) Imports: methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices LinkingTo: cpp11, BH(>= 1.62.0-1) Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: 61a55d5be8edbc7dca01202168dd22e6 Package: openPrimeR Version: 1.34.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: acc2a7c86b893f810562f4966a8e8cf6 Package: OpenStats Version: 1.24.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 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BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 0f8765015bee5f9db3429d8baf753e9d Package: OrderedList Version: 1.84.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 2184e48d27c2ba0af6888a420f78ae28 Package: ORFhunteR Version: 1.20.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: e89abc4804cefba1eb27900500d69c23 Package: ORFik Version: 1.32.0 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 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License: MIT + file LICENSE MD5sum: 11946bc16b9939722fb23b738dd926f9 Package: OSAT Version: 1.60.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 61982e0e810061081b066c62f8935e96 Package: Oscope Version: 1.42.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 647652a044d3b6b79525b3bc4d9cc9d1 Package: OSTA.data Version: 1.4.0 Depends: R (>= 4.5) Imports: osfr, utils, BiocFileCache Suggests: BiocStyle, DropletUtils, knitr, VisiumIO, SpatialExperimentIO License: Artistic-2.0 MD5sum: 03fba8f8ff385dd2596dee3e0c829ded Package: OTUbase Version: 1.62.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: fa7f99bf535b649be52ebd560aa8a9ba Package: OUTRIDER Version: 1.30.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, methods Imports: BBmisc, BiocGenerics, data.table, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, heatmaply, IRanges, matrixStats, pcaMethods, pheatmap, plotly, plyr, pracma, PRROC, RColorBrewer, reshape2, RMTstat, S4Vectors, scales, splines, stats, txdbmaker, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: file LICENSE MD5sum: b97555b41852d962898a6f9e4ff26dce Package: OutSplice Version: 1.12.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 5a0203d0cd43450600e7f214760ffb52 Package: OVESEG Version: 1.28.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 0943d5f7ea56f669d5da1c394009292d Package: PAA Version: 1.46.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: b199e847e0684f012a7c56dd8465a8c3 Package: packFinder Version: 1.24.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 6cc30f6ec0d8ac867827dc805d3bae58 Package: padma Version: 1.22.0 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 License: GPL (>= 3) MD5sum: 99f7b5be16f25621eaec3183a7de0517 Package: PADOG Version: 1.54.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: 69231cf57b94a34e3dd69132f7e02fd7 Package: pageRank Version: 1.22.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: e548882a88f1184d14197685af378fd1 Package: PAIRADISE Version: 1.28.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cbef19cdb6b509bf8dab3c5a386e6c31 Package: 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PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: 757a6fbe334500af528dcde00e1481ad Package: PathoStat Version: 1.38.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 57dc9112bb0b1485a771d5267fadc84c Package: pathRender Version: 1.80.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: e11709091a260ad74b149b4f25998644 Package: pathview Version: 1.52.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 7f0ee7829ea8648e7fd71ac75d324dd5 Package: 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methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 83caf3e8c8ca9291fc66f38d12de4e94 Package: pdInfoBuilder Version: 1.76.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: b705570e8177dabdf6a4650d2ab6730b Package: PeacoQC Version: 1.22.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) MD5sum: 2c51d193bb1970348911aa65563275b9 Package: peakCombiner 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Version: 1.48.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) MD5sum: cae8a5b2db3a9f077d3cb7424a8a13ad Package: peco Version: 1.24.0 Depends: R (>= 3.5.0) Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 1285306e047a58c68f49e105dc1bfcf7 Package: Pedixplorer Version: 1.8.0 Depends: R (>= 4.4.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl, DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui, shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr Suggests: diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools, R.devices, usethis, rlang, magick, cowplot License: Artistic-2.0 MD5sum: 0867646af3c3104b63121b214308f6eb Package: pengls Version: 1.18.0 Depends: R (>= 4.5.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 3b856b94c62eac1f5d9ff953c37736a2 Package: PepSetTest Version: 1.6.0 Depends: R (>= 4.1.0) Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr License: GPL (>= 3) MD5sum: 06a8e2800357d388c3858cb3e7d12a18 Package: PepsNMR Version: 1.30.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: a35cfb0b8ab7ec39aac07cab6a2e70ac Package: pepStat Version: 1.46.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 7bd8edc0c488e047fcb4052eb0636139 Package: pepXMLTab Version: 1.46.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c3c0be280e1866e40bc0701955b28247 Package: periodicDNA Version: 1.22.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, Seqinfo, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: ee55ae877d6d2deab1ef770b14ecf920 Package: pfamAnalyzeR Version: 1.12.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 97f4d6e2b1d97175db2d38d0e3b5003d Package: pgca Version: 1.36.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: c55584e993ced94606acabbf9839e4d9 Package: pgxRpi Version: 1.7.0 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: 7699b5445750f31020ac845894fd3cd2 Package: phantasus Version: 1.32.0 Depends: R (>= 4.3) Imports: ggplot2, protolite, Biobase, GEOquery, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: f18d278fd5a07bffb72b10f4441444f2 Package: phantasusLite Version: 1.10.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: 9dfe997b1e4a16266be78e4a2808eae6 Package: PharmacoGx Version: 3.16.0 Depends: R (>= 4.1.0), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: 57c85a72544bf14ee02699e6a5f579fc Package: PhenoGeneRanker Version: 1.20.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: ff8c0fc0c0d45860450379050e5bd799 Package: phenomis Version: 1.14.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: b8cd1b5763be30dba78c6cbcc4e33296 Package: phenopath Version: 1.36.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: c45c6f4c02527bda5861673b6a3afb77 Package: phenoTest Version: 1.60.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: fcd42d594985139c344ccfe37252e945 Package: philr Version: 1.38.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: e2c403ce3af45efddaabd14ca249cd28 Package: PhIPData Version: 1.20.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: d056f3d960632b2b7ddcf143d35415e2 Package: phosphonormalizer Version: 1.36.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 41e98e326334c26d30c768e7f71e0860 Package: PhosR Version: 1.22.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: b8115dd87738c55c6908021b93f29fd2 Package: PhyloProfile Version: 2.4.6 Depends: R (>= 4.5.0) Imports: ape, bioDist, BiocStyle, Biostrings, bit64, bsplus, colourpicker, data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra, htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, scattermore, shiny, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 8f43d7a6a4cd9e04f565ddb71ae49e59 Package: phyloseq Version: 1.56.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7-4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5) Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Enhances: doParallel (>= 1.0.10) License: AGPL-3 MD5sum: cc9b949a7d0bd5241b71098dbee9b2f4 Package: piano Version: 2.28.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 80b3b3df2242f758ac0faf1093923140 Package: PICB Version: 1.4.0 Imports: utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: 8d49b1279ceaf40523c58792e917b492 Package: pickgene Version: 1.84.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 6d74908c77293d414553aa1efa379949 Package: Pigengene Version: 1.38.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 0f03e330838e99af0155be89417be8b4 Package: pipeComp Version: 1.22.1 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 85bf498ab4043db5939777737bd10bce Package: pipeFrame Version: 1.28.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, Seqinfo, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 6bf89660138195d87b194f0c8229385f Package: PIPETS Version: 1.8.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: bccfee8031b0b79ead4d13264355d451 Package: Pirat Version: 1.6.0 Depends: R (>= 4.5.0) Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: 08c99929d9704597cf594a52ebea6341 Package: PIUMA Version: 1.8.0 Depends: R (>= 4.3) Imports: Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne, kernlab, vegan, dbscan, grDevices, stats, methods, SummarizedExperiment, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, Seurat, SingleCellExperiment, aricode, mclust, viridis, magick, ggrepel, dplyr License: GPL-3 + file LICENSE MD5sum: 199de76a53d3652cc923bef0c22fdba7 Package: plaid Version: 1.0.1 Depends: R (>= 4.3.3) Imports: Matrix, MatrixGenerics, matrixStats, methods, collapse, qlcMatrix, GSVA, fgsea, SummarizedExperiment, BiocSet, stats, utils Suggests: BiocStyle, knitr, rmarkdown, sparseMatrixStats, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3a8633768944efadbe160470da06a556 Package: planet Version: 1.20.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: bf15e53bbda2ea5ce0933d3632635d99 Package: planttfhunter Version: 1.12.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1d5f5ecf210bc20f79ae6b8a80e680e2 Package: plasmut Version: 1.10.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: c07f27f2783c5ee34aee8a3d19b9af5c Package: plgem Version: 1.84.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: c03d519ac0f593f809fd6d9cda0344eb Package: plier Version: 1.82.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 6faafd22b2563af6362b137816eec089 Package: PlinkMatrix Version: 1.0.0 Depends: R (>= 4.1.0), methods, Rcpp, DelayedArray, SummarizedExperiment Imports: BiocFileCache, GenomicRanges, IRanges LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat, rmarkdown, irlba, GenomeInfoDb License: MIT + file LICENSE MD5sum: 35781cffe92283aec69e9c55447e5573 Package: plotgardener Version: 1.18.0 Depends: R (>= 4.2.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene License: MIT + file LICENSE MD5sum: f402b0f19b00301f9bae761bcfbf8c75 Package: plotGrouper Version: 1.30.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: ce7dc8b0cf0d1d355b05b6edb172ed9d Package: PLPE Version: 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Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, Seqinfo, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomeInfoDbData, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: c3059a954e87225d1e53a9fd2a0f29d0 Package: QuaternaryProd Version: 1.46.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: 64d1da014eb4de0973d279ecf845951c Package: QUBIC Version: 1.40.0 Depends: R (>= 4.5.0) Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 2870970ae10048c5dc3d061e165fb513 Package: queeems Version: 1.0.0 Depends: R (>= 4.5.0), 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MD5sum: 3d9369a34a5388a98901d3e193f6282e Package: raer Version: 1.10.0 Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli LinkingTo: Rhtslib Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE MD5sum: ba1652d90947b224fadc105f01f86e5a Package: RaggedExperiment Version: 1.36.0 Depends: R (>= 4.5.0), GenomicRanges (>= 1.61.1) Imports: BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment (>= 1.39.1), utils Suggests: BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb, MultiAssayExperiment 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BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 5263d9c2cbccc8617115736e4d064439 Package: retrofit Version: 1.12.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: a201c39bb9b45e172d50330fe97bc51b Package: ReUseData Version: 1.12.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 2998ab88ab362deb36300021b6931274 Package: rexposome Version: 1.34.2 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: 81850d4664e84f45b41a5acb74d05669 Package: rfaRm Version: 1.24.1 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: 4b9527f7a592cd834f80e7db5020ef62 Package: Rfastp Version: 1.22.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: fda3d0b309566825a51bc0625cd86d8e Package: RFLOMICS Version: 1.4.2 Depends: R (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment, shinyBS, dplyr, ggplot2, htmltools, knitr, coseq Imports: vroom, org.At.tair.db, AnnotationDbi, clusterProfiler, ComplexHeatmap, data.table, DT, edgeR, FactoMineR, ggpubr, ggnetwork, ggrepel, grDevices, grid, httr, limma, magrittr, methods, mixOmics, MOFA2, plotly, purrr, RColorBrewer, reshape2, reticulate, rmarkdown, S4Vectors, shiny, shinydashboard, shinyWidgets, stats, stringr, tidyr, tibble, tidyselect, UpSetR, Suggests: testthat, shinytest2, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: 8c9a5156b658d162e3517046a468f3ec Package: rfPred Version: 1.50.0 Depends: R (>= 3.5.0), methods Imports: utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: f530cba87d8b9392a9360e7a5246a483 Package: rGenomeTracks Version: 1.18.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 22be8f081f56273036ea4e9cb2c76435 Package: rgoslin Version: 1.16.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 737935c70420e77f40eef9d8b6a6bb69 Package: RGraph2js Version: 1.40.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: 6e4f6a715a83c25b5817f2abacda8261 Package: Rgraphviz Version: 2.56.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 68009afadf18c841000fc975603c86bf Package: rGREAT Version: 2.14.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: 2a3457ec41ef33e927361b66d676a71f Package: RGSEA Version: 1.46.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 3e2daaf792ed6f71a65696e062ba7be5 Package: rgsepd Version: 1.44.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: f190e72adedef2fb9e15fb2ede340793 Package: rhdf5 Version: 2.56.0 Depends: methods, R (>= 4.0.0) Imports: rhdf5filters (>= 1.15.5), Rhdf5lib (>= 1.33.3) LinkingTo: Rhdf5lib Suggests: bench, BiocParallel, BiocStyle, bit64, curl, dplyr, ggplot2, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: 22416e0d442f28c976869cff92db0f14 Package: rhdf5client Version: 1.34.2 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: c7b040f481277c64bf3ce77dcfdff1c4 Package: rhdf5filters Version: 1.24.1 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, testthat, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE MD5sum: 80f000bbfd6c175ce97e48a7fa30e0e7 Package: Rhdf5lib Version: 2.0.0 Depends: R (>= 4.2.0) LinkingTo: biocmake Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: 6f08f5be975e644d5115d6e876570023 Package: rhinotypeR Version: 1.6.0 Depends: R (>= 4.5.0) Imports: Biostrings, methods, MSA2dist, msa Suggests: knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 97014da9590de684ab3adf8b98785cc7 Package: Rhisat2 Version: 1.28.1 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 8ee8d63a7e293b1719ab693fae4c5087 Package: Rhtslib Version: 3.8.0 Imports: tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: 01938b889dd0d8696de26fcbb6029d80 Package: RiboCrypt Version: 1.18.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, ComplexHeatmap, cowplot, crosstalk, data.table, dplyr, DT, fst, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, grid, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, rclipboard, RCurl, rtracklayer, shiny, shinycssloaders, shinyhelper, shinyjs, shinyjqui, shinyWidgets, stringr, writexl Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 95398c626089f059ed3565048a4a34d8 Package: RiboDiPA Version: 1.20.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: a0dfff45062874935f1626aa6f6f32d2 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testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: b84bc5f3e587cb82d07d9233a24912ce Package: rifi Version: 1.16.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: b452be42e3ecfe4e49572edc507305d1 Package: rifiComparative Version: 1.12.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 0cfe15b31e639e90ce0678bd130eaf91 Package: Rigraphlib Version: 1.4.0 LinkingTo: biocmake Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: ad24169cac39f28fefaf414fb1a3c745 Package: rigvf Version: 1.4.1 Depends: R (>= 4.1.0) Imports: methods, httr2, rjsoncons, dplyr, tidyr, rlang, memoise, cachem, whisker, jsonlite, GenomicRanges, IRanges, Seqinfo Suggests: knitr, rmarkdown, testthat (>= 3.0.0), plyranges, plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, tibble License: MIT + file LICENSE MD5sum: fe0d82d08cb57ac52ece08fd7b25602d Package: RImmPort Version: 1.40.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 7a600df32b10690dd6b85df50c1daa08 Package: RITAN Version: 1.36.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: 7c242101f6ba2fac85edba3a35c81158 Package: RIVER Version: 1.36.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: 2d59964e29046dacaf7978edc87c519b Package: RJMCMCNucleosomes Version: 1.36.0 Depends: R (>= 3.5), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, Seqinfo, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 7ac5d502d54b760c3ce49adec173fe08 Package: RLassoCox Version: 1.20.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 MD5sum: 7c9d55891edff31d546514464bb69564 Package: RLMM Version: 1.74.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: 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R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, apeglm, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 4bb0e1f91dada2052b89fc2d66fb922a Package: rmspc Version: 1.18.0 Imports: processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3a5db48687018248c34df303103bbcee Package: RNAAgeCalc Version: 1.24.0 Depends: R (>= 3.6) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 03fe63276367a4407d29ec479718ae59 Package: RNAdecay Version: 1.32.0 Depends: R (>= 4.3) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 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Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: 95abcac7aab9e8849694d9c6095998d9 Package: ROC Version: 1.88.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: 56f57625637cf2460b9025a10cdf7216 Package: ROCpAI Version: 1.24.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 320de038f3a3d16ae7dff943d46c41cc Package: RolDE Version: 1.16.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: 4d665f85978800cb16a6dded55330f0e Package: rols Version: 3.7.1 Depends: methods, R (>= 4.1.0) Imports: httr2, jsonlite, utils, Biobase Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 MD5sum: 3518bc1480ab4a38c3eb5999c8c7c123 Package: ROntoTools Version: 2.40.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 3fb56474fb3669f53a1a5e22ff87011c Package: ropls Version: 1.44.0 Depends: R (>= 3.5.0) Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis, rmarkdown, testthat License: CeCILL MD5sum: d5e143604fa0c421dad120283891929b Package: ROSeq Version: 1.24.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 1388613cdb9f776a20af3cd538d9046d Package: ROTS Version: 2.4.0 Depends: R (>= 3.6) Imports: Rcpp, stats, Biobase, methods, BiocParallel, lme4, survival LinkingTo: Rcpp Suggests: testthat License: 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Version: 1.46.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 2b21fbb7c8da3d07629cf689ecb60c7e Package: rqt Version: 1.38.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: e01138e6bd41fb785d36a98f8b1f178c Package: rqubic Version: 1.57.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: ec5543195168db4000c7d4ce27a7fc51 Package: RRHO Version: 1.52.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: 87fcaac717e5a8bfbf5957b841db3e0f Package: rrvgo Version: 1.24.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 52578f8102dd30cd3ec9bad8141ee8e6 Package: Rsamtools Version: 2.28.0 Depends: R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 6b137389c72a76e6934e4b92434b8c4b Package: rScudo Version: 1.28.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 4b8d0c3522f3df30bd1259a547b92199 Package: rsemmed Version: 1.22.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 55d17b60fb28aa6900d6a1cde3be7548 Package: RSeqAn Version: 1.32.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: a8ad57c2d7c2fbe816cc281e016d7dcb Package: Rsubread Version: 2.26.0 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 3bb5b78d61475f4d9031297037910396 Package: RSVSim Version: 1.52.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign License: LGPL-3 MD5sum: 97c9ea08ce67d0de495d5d8e465b6f3e Package: rSWeeP Version: 1.24.0 Depends: foreach, doParallel, parallel, Biostrings, methods, utils Imports: tools, stringi, Suggests: Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 534f43d79b018b39d7c9d21875cffc15 Package: RTCA Version: 1.64.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 8f700c8452390cd7f4daed3a8672efc6 Package: RTCGA Version: 1.41.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: e7259ae85698e529355789093ad35eec Package: RTCGAToolbox Version: 2.42.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, Seqinfo, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors, stats, stringr, SummarizedExperiment, TCGAutils, utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: e698fbe8257c92c8246d6489a33b2f79 Package: RTN Version: 2.36.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 52663eef6047f356e551dcc7e1db09ba Package: RTNduals Version: 1.36.0 Depends: R(>= 4.4.0), RTN(>= 2.32), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 8e6f2f38b762ac0ad39daecec2520080 Package: RTNsurvival Version: 1.36.0 Depends: R(>= 4.4.0), RTN(>= 2.32), RTNduals(>= 1.32), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: fbed0c1a17d1062198ca5dc5905989e8 Package: RTopper Version: 1.58.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 836bb7415843403a7ef814456081caf4 Package: Rtpca Version: 1.22.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: 6737fe7d632ba4be7ecf65f288e00fbb Package: rtracklayer Version: 1.72.0 Depends: R (>= 3.5), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), Seqinfo, Biostrings (>= 2.77.2), curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: GenomeInfoDb, BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: c201a6c81aa78edb5e026043c14fc43c Package: rTRM Version: 1.50.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d69793b7c5df1f173265c1f045010f4a Package: rTRMui Version: 1.50.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 43b7b95e541a0648dd55d0abb3ca4464 Package: RUCova Version: 1.4.0 Depends: R (>= 4.4.0) Imports: dplyr, fastDummies, ggplot2, stringr, tibble, Matrix, ComplexHeatmap, grid, circlize, SingleCellExperiment, SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors Suggests: knitr, rmarkdown, BiocManager, BiocStyle, remotes, ggpubr, ggcorrplot, ggh4x, testthat (>= 3.0.0) License: GPL-3 MD5sum: ae6043e5aac7cbcf6f4fd6ffaac7d1c2 Package: RUVcorr Version: 1.44.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: 800bf67f41539bb7644ccb5baa91fb90 Package: RUVnormalize Version: 1.46.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 22f3820b444de06fb2af1d98481a17c0 Package: RUVSeq Version: 1.46.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: 891db9a8cc0893d2519a5eb291a29413 Package: Rvisdiff Version: 1.10.0 Depends: R (>= 4.5.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: cd40e592535709809f46de009324d87b Package: RVS Version: 1.34.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: ddab8793f8fce8f001ce48e06f12c0ce Package: rWikiPathways Version: 1.32.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3acff778aa01b74bc343547cbdf088c3 Package: S4Arrays Version: 1.12.0 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors (>= 0.47.6), IRanges Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, HDF5Array, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3e592597e0bcbff7c34ff21380ad8d7c Package: S4Vectors Version: 0.50.2 Depends: R (>= 4.1.0), methods, utils, stats, stats4, BiocGenerics (>= 0.53.2) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2426af1ad59a940e1fc4112955f06228 Package: safe Version: 3.52.1 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: 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Package: SANTA Version: 2.48.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: c7f828e0724031b23bd862b06d14088c Package: sarks Version: 1.24.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: b885196762285ea5cdd2c0198c6b416f Package: saseR Version: 1.8.0 Depends: R (>= 4.3.0) Imports: ASpli, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr, edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges, igraph, IRanges, limma, methods, MASS, MatrixGenerics, S4Vectors, stats, SummarizedExperiment, parallel, PRROC Suggests: rrcov, knitr, txdbmaker License: Artistic-2.0 MD5sum: 6a9f5ed9e5ee81303b32f09fba8244ce Package: satuRn Version: 1.20.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: f09c2ab092bd52d0afe39f386ecc208c Package: SBGNview Version: 1.26.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: fbfb7d6c13eaf27a9b789f40a3881046 Package: SBMLR Version: 2.8.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: 381bac751391a10abfa217933a33c9b0 Package: SC3 Version: 1.40.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 9b62e0196d92a5ed208f49e60efe851b Package: scafari Version: 1.2.0 Depends: R (>= 4.5.0) Imports: magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: LGPL-3 MD5sum: b6237c7be77cc796ebe190360bc96913 Package: Scale4C Version: 1.34.0 Depends: R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 0bab38191951782070318b72af230e28 Package: ScaledMatrix Version: 1.20.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: 70261f127ae47e744caa0217ca4bbff4 Package: SCAN.UPC Version: 2.54.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 74412365c0073cbe3033936bc9c2d26f Package: scanMiR Version: 1.18.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 503f530edab096370a133759506e1b28 Package: scanMiRApp Version: 1.18.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 13578a19352044190d0fc42a6145f972 Package: scAnnotatR Version: 1.18.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 2d15e0b9fff807207f0c336efdfef6ef Package: SCANVIS Version: 1.26.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: c16bea82a8b550d508614a534482c24d Package: SCArray Version: 1.20.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.31.5) Imports: S4Vectors, utils, Matrix, SparseArray (>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: 9d6354e036e42f756d6f4f7b7c87274a Package: SCArray.sat Version: 1.12.0 Depends: methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: 52ce9208fdd3f201659631c103b31799 Package: scater Version: 1.40.2 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore, ggrastr, MASS License: GPL-3 MD5sum: f80cabc48185538ee326a5115fb9fdbd Package: scatterHatch Version: 1.18.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: c1a7f782d8d693179eabdd34fb0f717a Package: scBFA Version: 1.26.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: b270343bf30d59b8193307003fa834ad Package: SCBN Version: 1.30.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: d06257bcad60a2ff87efba8ed29fe39a Package: scBubbletree Version: 1.14.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 9eaea5f0aeb513ed123c07422b2984e5 Package: scCB2 Version: 1.22.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 6bd7c14346025724ca473d607f570074 Package: scClassify Version: 1.24.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 7d72ed55ba95d411b195281b14b5bf68 Package: sccomp Version: 2.4.0 Depends: R (>= 4.3.0), instantiate (>= 0.2.3) Imports: stats, boot, utils, scales, lifecycle, rlang, tidyselect, magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble, ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, loo, prettydoc, SeuratObject, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: 4f49658df2682044aa2440ed9ec4cd87 Package: scConform Version: 1.0.0 Depends: R (>= 4.5.0) Imports: igraph, stats, SummarizedExperiment, BiocParallel, Rgraphviz Suggests: knitr, Matrix, rmarkdown, BiocStyle, VGAM, ontoProc, MerfishData, doParallel, scuttle, SingleCellExperiment, scran, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 65c6d14f30fed490ffbcb64fe5951842 Package: scDataviz Version: 1.22.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: d85a49c686aa4eb0ae446faa6f3850a2 Package: scDblFinder Version: 1.26.7 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scater, scuttle, scrapper, scran, bluster, methods, DelayedArray, xgboost (>= 3.1), stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: a5da02b80a879ee05c957acd86cb97c1 Package: scDD Version: 1.36.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 203ac660fce4a13aff9f827fd590da2c Package: scDDboost Version: 1.14.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 26f3272b41ea557ede2391e74146b897 Package: scde Version: 2.40.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 04b2ab4ba0bba5c1f5eae9694311c8e5 Package: scDesign3 Version: 1.10.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, rvinecopulib, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: 7906b01f80872314c9a0538fd8ae2a0f Package: scDiagnostics Version: 1.6.1 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2, GGally, ggridges, SummarizedExperiment, ranger, transport, cramer, rlang, bluster, scales, MASS, stringr, Matrix, grDevices Suggests: AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid, ragg, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 871b7c6a622c36dc374564e819031496 Package: scDotPlot Version: 1.6.0 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: bdc836442a6264b28ca890af684e696d Package: scds Version: 2.0.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: b59f6dd607287e4c17b4c7617e428a12 Package: scECODA Version: 1.0.1 Depends: R (>= 4.6.0) Imports: BiocGenerics, cluster, corrplot, DESeq2, dplyr, factoextra (>= 2.0.0), ggplot2, ggpubr, ggrepel, gtools, Matrix, mclust, methods, pheatmap, plotly, rlang, rstatix, S4Vectors, stringr, SummarizedExperiment (>= 1.34.0), tidyr, vegan Suggests: Seurat (>= 5.0.0), igraph, knitr, rmarkdown, BiocStyle, testthat, scRNAseq License: GPL-3 + file LICENSE MD5sum: a2892decbe6d8799ebe6ba26a7bb538c Package: SCFA Version: 1.22.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: a4901f92c505d25a4de2981dcc656aa4 Package: scFeatureFilter Version: 1.32.0 Depends: R (>= 4.5.0) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, MASS, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: f5a4c5fe29900f39c173faba3dd50203 Package: scFeatures Version: 1.12.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler, pheatmap, limma, ggplot2, plotly, igraph, data.table, enrichplot, DOSE, rmarkdown License: GPL-3 MD5sum: 1b491f5a7f4ef1ecd8c38a557dff9efb Package: scGPS Version: 1.26.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 53700667bb33efc18266492e39404440 Package: scGraphVerse Version: 1.2.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG, GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, distributions3, dplyr, grDevices, graphics, httr, igraph, jsonlite, methods, parallel, reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors, graph, mpath Suggests: AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot, fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db, org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA, rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0), knitr, rmarkdown, tidyverse, magick, celldex, SingleR, TENxPBMCData, scater, GenomeInfoDb, GenomicRanges, License: GPL-3 + file LICENSE MD5sum: 266f8ffec4ebfa08d57b27c41a504217 Package: schex Version: 1.26.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 81d4f0257db5d0de43b31a6bf11a665a Package: scHiCcompare Version: 1.4.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: de3bfb806681d0712bdfdb52c34d013f Package: scHOT Version: 1.24.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: ba4d10397e23c23eef6bde0a75322e0a Package: scider Version: 1.9.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 426031953b9c9dad9cdf10ffa5fc51a3 Package: scifer Version: 1.14.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, basilisk.utils, reticulate, here, pwalign, utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: c8b66b19c92aa5cb54bd97ad71312092 Package: scLANE Version: 1.2.0 Depends: glm2, magrittr, R (>= 4.5.0) Imports: geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr, furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2, splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr, tidyselect, broom.mixed, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba, rlang, magick, igraph, scater, gtable, ggpubr, viridis, bluster, cluster, circlize, speedglm, rmarkdown, gridExtra, BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel, BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0), testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment License: MIT + file LICENSE MD5sum: 4cbcb7fbf604cfed34898d01db802737 Package: scLang Version: 1.0.0 Imports: dplyr, ggplot2, henna, methods, paletteer, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment Suggests: BiocStyle, knitr, qs2, rmarkdown, scater, scRNAseq, Seurat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5a4e5b1588b147948ccadd7f2494c568 Package: scmap Version: 1.34.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ace013ccd6df14651feaa02b55872aac Package: scMerge Version: 1.28.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: 00b240ca0a7397a1016da657168b7dfe Package: scMET Version: 1.14.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: f88828b23aa18fde43d82e308f662242 Package: scmeth Version: 1.32.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, bsseq, AnnotationHub, Seqinfo, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, ggplot2, ggthemes License: GPL-2 MD5sum: 93a8b00738015ad68ad8d8ddb5f7dafb Package: scMitoMut Version: 1.8.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 85755bf9d181970bac98761725d06546 Package: scMultiSim Version: 1.8.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 0eaf5c6270ae736bcd3c8bd52246e2f1 Package: SCnorm Version: 1.34.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 3dc87cf31438bb130aa018ab611330c6 Package: scone Version: 1.36.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6) Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: cbd5a942487a09f1878b2ae84e5736f1 Package: Sconify Version: 1.32.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 07ce1aef2a6084a6af1ccb72fbc95ae4 Package: SCOPE Version: 1.24.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 8c616666ddd21ba0f8d43d6cb3182383 Package: scoreInvHap Version: 1.34.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 93a07070459e04a04937fac2b34afddc Package: scoup Version: 1.6.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 2492f0449937b73074d65d3603bc8b85 Package: scp Version: 1.22.0 Depends: R (>= 4.3.0), QFeatures (>= 1.19.1) Imports: IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot License: Artistic-2.0 MD5sum: 0383e11713c0649eaa8da18fe9d49846 Package: scPassport Version: 1.0.0 Depends: R (>= 4.3) Imports: shiny, miniUI, Rcpp, S4Vectors LinkingTo: Rcpp Suggests: Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 0a92ce2e020833700f2108d3120f94f4 Package: scPCA Version: 1.26.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 23f27adb0614b129757dbda12990e8cb Package: scPipe Version: 2.12.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: e0d59ce2016ced1781d5c5d0e6cd4cfb Package: scQTLtools Version: 1.4.0 Depends: R (>= 4.4.1.0) Imports: ggplot2(>= 3.5.1), Matrix (>= 1.7-0), stats (>= 4.4.1), progress(>= 1.2.3), stringr(>= 1.5.1), dplyr(>= 1.1.4), SeuratObject(>= 5.0.2), methods(>= 4.4.1), magrittr(>= 2.0.3), patchwork(>= 1.2.0), DESeq2 (>= 1.45.3), VGAM (>= 1.1-11), limma (>= 3.61.9), biomaRt(>= 2.61.3), gamlss (>= 5.4-22), SingleCellExperiment(>= 1.27.2), SummarizedExperiment(>= 1.32.0), yulab.utils (>= 0.2.3) Suggests: BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db, org.Ce.eg.db, org.At.tair.db, testthat (>= 3.2.1.1) License: MIT + file LICENSE MD5sum: 95a7ecc099c9ab7bcb5141dbc332f05d Package: scran Version: 1.40.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater, scrapper License: GPL-3 MD5sum: 65b513a9dfb007fd6f32c0aa644c9787 Package: scrapper Version: 1.5.17 Imports: methods, Rcpp, beachmat (>= 2.25.1), S4Vectors, SparseArray, DelayedArray, BiocNeighbors (>= 1.99.0), parallel LinkingTo: Rcpp, assorthead (>= 1.5.3), beachmat, BiocNeighbors, Rigraphlib Suggests: testthat, knitr, rmarkdown, BiocStyle, Matrix, IRanges, SummarizedExperiment, SingleCellExperiment, scRNAseq, org.Mm.eg.db, scater, igraph License: MIT + file LICENSE MD5sum: ac1fd443bce4833adb66ce2b082e8fc9 Package: scReClassify Version: 1.18.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: c9f3d8cc9fef3376ad0af3946d4ee2ff Package: scRecover Version: 1.28.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 7e9279f04a3b351638cc3f9be2247650 Package: screenCounter Version: 1.12.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 20e559a133a56905e34a373ccef6b6c3 Package: ScreenR Version: 1.14.0 Depends: R (>= 4.3) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), markdown, knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: b340f1f40a41056453408ee8544ece7c Package: scRepertoire Version: 2.8.0 Depends: ggplot2, R (>= 4.0) Imports: dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, immApex, iNEXT, Matrix, quantreg, Rcpp, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, SummarizedExperiment, tidygraph, purrr, lifecycle, methods LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, Peptides, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d8c6d605c6586ba4d962bf9b5931ba83 Package: scRNAseqApp Version: 1.12.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, desc, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggnewscale, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle, shinytest2 Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle, terra License: GPL-3 MD5sum: 1aa52c4e97b4f8f11224cec5fcd07bd2 Package: scruff Version: 1.30.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly, patchwork Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 9e837e70bfe04e6ce1e2862a20895586 Package: scry Version: 1.24.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 82d88f7c3649322dc03e133ed376f8d5 Package: scShapes Version: 1.18.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7818dfaf128c13e98462064fa105257c Package: scTensor Version: 2.22.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 5cbd53a052ae211af32132a0b9249255 Package: scTGIF Version: 1.26.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: 09657c17d3532f684662faaf78480d55 Package: scTHI Version: 1.24.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 2770f475bfb68f4f7221e500f064bcb8 Package: scToppR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: dplyr, forcats, ggplot2, stringr, openxlsx, viridis, patchwork, utils, httr2 Suggests: airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f2a58a4a332f2ab4981f409048933b25 Package: scTreeViz Version: 1.18.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: c2fdd2cfe4f2c398f124d3bef0f2ce7f Package: scTypeEval Version: 1.0.0 Depends: R (>= 4.5.0) Imports: Matrix (>= 1.6-5), BiocParallel (>= 1.34.2), dplyr (>= 1.1.4), tidyr (>= 1.3.1), scran (>= 1.30.2), bluster (>= 1.12.0), ggplot2 (>= 3.5.1), ggrepel (>= 0.9.6), cluster (>= 2.1.4), SingleR (>= 2.4.1), irlba (>= 2.3.5.1), transport (>= 0.15-4), grDevices, methods, stats, utils Suggests: testthat (>= 3.0.0), transformGamPoi (>= 1.8.0), glmGamPoi (>= 1.14.3), anndata (>= 0.8.0), SummarizedExperiment (>= 1.32.0), igraph (>= 2.1.1), Seurat, SingleCellExperiment, knitr, rmarkdown, BiocStyle, BiocManager, SeuratObject, ggpubr, rlang, stringr, tibble License: GPL-3 + file LICENSE MD5sum: f837162e34443a77fda120577a020add Package: scuttle Version: 1.22.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: a361ae6055ac1cb2c015c0679edc0372 Package: scviR Version: 1.12.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: 3aa0b1f7c66d52516f147423460e7613 Package: SDAMS Version: 1.32.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: de8985178302419f2e0edb749c8c35b9 Package: seahtrue Version: 1.6.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1), janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>= 1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>= 0.5.6), readr (>= 2.1.5), scales (>= 1.3.0) Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: d4ba7d9c881bfa82107abd8be3541e58 Package: sechm Version: 1.20.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 5d0b2915a65c8e6476db843192ca3409 Package: segmenter Version: 1.18.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: 8022ee2330931f4a689bf869af1c5405 Package: segmentSeq Version: 2.46.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: 0da3e9f4791ffaf4fb90c7d0fee486c2 Package: selectKSigs Version: 1.24.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 62eed1b4e0b00307f8f0978e27f8dea0 Package: SELEX Version: 1.44.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: 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Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 4df0fcccf8d84a737267e979884a528a Package: seq2pathway Version: 1.44.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 5b243e56856ff7544575468258a31a25 Package: SeqArray Version: 1.52.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 75cb1a06b32ae34b4a578973363309c3 Package: seqCAT Version: 1.34.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: c95cffd91e451afa7f0c47ab557f9a22 Package: seqcombo Version: 1.34.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: bf5895986c77f4c2502dbf1eb2f8fedd Package: SeqGate Version: 1.22.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 823a7981d86a204ecb5ffef30448a6e6 Package: SeqGSEA Version: 1.52.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: c20fa499becc534fa14143397bb5ac01 Package: Seqinfo Version: 1.2.0 Depends: methods, BiocGenerics Imports: stats, S4Vectors (>= 0.47.6), IRanges Suggests: GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d241c77ba514701b3ad902f9cdc84c55 Package: seqLogo Version: 1.78.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 9dcf796ccc23356359cb8d34f34ea02c Package: seqPattern Version: 1.44.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 547d54ac08a89e32fdb4d16b1d42333b Package: seqsetvis Version: 1.32.0 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, Seqinfo, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, GenomeInfoDb, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 7209dab0401db737a926fad20bdca33b Package: SeqSQC Version: 1.34.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: cd4ee4a9e8395d856f15a68fdc54fb05 Package: Seqtometry Version: 1.0.1 Depends: R (>= 4.5.0) Imports: BiocSingular, checkmate, data.table, DelayedMatrixStats, future.apply, Matrix, MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, sparseMatrixStats, zeallot LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS, patchwork, rmarkdown, scater, scuttle, SingleCellExperiment, stringr, TENxPBMCData, testthat (>= 3.0.0), tibble License: MIT + file LICENSE MD5sum: 0601aa5986dc1618a01f35ce0c6e0bd9 Package: SeqVarTools Version: 1.50.1 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: ac5b988c093d16e2890b333eb34a3b71 Package: SEraster Version: 1.4.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes License: GPL-3 MD5sum: 7295cc9ade12a7994ded320031d3db09 Package: sesame Version: 1.30.1 Depends: R (>= 4.5.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1), IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, Seqinfo, stats, SummarizedExperiment (>= 1.39.1), dplyr, reshape2 Suggests: scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: 48fa455fefa2b36adf23c359e9d5fd3f Package: SETA Version: 1.2.0 Depends: R (>= 4.5.0) Imports: dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats, tidygraph, rlang, utils Suggests: BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6571c7873a284e1f7393359b852d5a47 Package: SEtools Version: 1.26.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: d6e4f35558e58e6176d2076a15ae6289 Package: sevenbridges Version: 1.42.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 2f59fb4f5681a14966d5c5d02ee3d5ec Package: sevenC Version: 1.32.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), Seqinfo, GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: 0561f7f4fd3b4284cf6e5de33a2e116d Package: sfi Version: 1.0.0 Depends: R (>= 4.5.0) Imports: Rcpp, enviGCMS, stats, mzR, rmarkdown, methods, SummarizedExperiment, S4Vectors LinkingTo: Rcpp Suggests: knitr, data.table, BiocStyle, ggplot2, MsCoreUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a514ed5426c6881ac7443d433779100c Package: SGCP Version: 1.11.0 Depends: R (>= 4.2.0) Imports: ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle License: GPL-3 MD5sum: 6266690fa0644d48682d466068cf6767 Package: SGSeq Version: 1.46.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), Seqinfo, grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 989e1157910a57e32d16759da4295200 Package: SharedObject Version: 1.26.2 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 201b62a46c56bf34fdb3d2c25081b65d Package: shiny.gosling Version: 1.8.0 Depends: R (>= 4.1.0) Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 2c275e2751d135923e074bf4567234fd Package: shinybiocloader Version: 1.2.0 Depends: htmltools Imports: shiny Suggests: shinydashboard, tinytest, quarto License: Artistic-2.0 MD5sum: 263ec6db5d35321241257167445791c5 Package: shinyDSP Version: 1.4.0 Depends: R (>= 4.5) Imports: AnnotationHub, BiocGenerics, bsicons, bslib, circlize, ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub, ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma, magrittr, pals, readr, S4Vectors, scales, scater, shiny, shinycssloaders, shinyjs, shinyvalidate, shinyWidgets, SingleCellExperiment, standR, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, withr Suggests: BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 275d830e34c0e5d7c4bece5691e7ebab Package: shinyepico Version: 1.20.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: 0e36e98e8655090102ad3c20e94d5baa Package: shinyMethyl Version: 1.48.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 8fc31345de7dbf91396a8b8a0231bde9 Package: ShortRead Version: 1.70.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 22d2ad5db72e615af553de4c77ef1415 Package: SIAMCAT Version: 2.16.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 01e0a7d2c51eb5cce75fa7f1dfe455a3 Package: SICtools Version: 1.42.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5af055d3312d0769c9ccb477e0360c3c Package: SigCheck Version: 2.44.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: fd68e02481f3ec090a59f07624569908 Package: sigFeature Version: 1.30.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: c6b4c39b5eb5d9fdbe7d938dcf8995c7 Package: siggenes Version: 1.86.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: ab598e0853be5dba879d15e6bc5ba66b Package: sights Version: 1.38.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 707e0093a2f28fb9f01bdc8dc0756abd Package: signatureSearch Version: 1.26.0 Depends: R(>= 4.5.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, readr, rhdf5, GSEABase, DelayedArray, GO.db, BiocGenerics, tibble, DOSE, AnnotationHub, stringr LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: 41d42a993ee5b2b6a52fb6f9fd1bdb61 Package: signeR Version: 2.14.0 Depends: R (>= 4.1.0), NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome, broom, VariantAnnotation LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: 09e2390509f0d9c50002c67fc783a0a4 Package: signifinder Version: 1.13.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 61fbdd716ea883d314aff080ed682504 Package: SigsPack Version: 1.26.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: a9427f4dcf0b5d56730bb2e3b7ff7dce Package: sigsquared Version: 1.44.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 1f34ab5cdc50d83e647ef32a37f8f48d Package: SIM Version: 1.82.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: d633e7ebe684faba68f8fff4178883b2 Package: SIMAT Version: 1.44.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 2bc58cf39ec84a6f058e0cca445e5774 Package: SimBu Version: 1.14.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 9d1a70e7e7139b6256a02ec089eb12ee Package: SIMD Version: 1.30.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: db901830bd27d03283f0ef2fa6f9e8a6 Package: SimFFPE Version: 1.24.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 265ed2c5de3506b335df7bb7080afe0a Package: similaRpeak Version: 1.44.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 2236344db3a4fca5d5df5fa880ea9dcc Package: SIMLR Version: 1.38.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 876e38b2f1f0c833fb5286f5f32cd666 Package: simona Version: 1.10.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: 18a143316d6cbf81f1ae35fd8699f2f1 Package: simPIC Version: 1.8.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick License: GPL-3 MD5sum: 8453a348c8ef7524c6c18680867dd018 Package: simpleSeg Version: 1.14.0 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: faa274227b62599057568abb8ae85fb4 Package: simplifyEnrichment Version: 2.6.0 Depends: R (>= 4.1.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 17c5f9bce97a68e7aa3eca0ff4c9ccd1 Package: sincell Version: 1.44.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 9605fc7f3551d72cf4c7c5b3c955b39b Package: singIST Version: 1.0.2 Depends: R (>= 4.5.0) Imports: msigdb, GSEABase, checkmate, stats, asmbPLS, BiocParallel, stringr, FactoMineR, Seurat, SeuratObject, biomaRt, data.table, purrr, SingleCellExperiment, SummarizedExperiment, scran, scuttle, missMDA, S4Vectors Suggests: testthat (>= 3.0.0), BiocStyle, knitr, qpdf, utils, RcppAlgos, glmGamPoi, methods, sp License: MIT + file LICENSE MD5sum: b261c64d736fd1cc70547d7e24f49812 Package: SingleCellAlleleExperiment Version: 1.8.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a133a510f1d750ddedc74ad4dc002f16 Package: SingleCellExperiment Version: 1.34.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 5f3ba90900cc46be46e230c29e344d30 Package: SingleCellSignalR Version: 2.2.0 Depends: R (>= 4.5) Imports: stats, utils, methods, ggplot2, matrixTests, matrixStats, foreach, BulkSignalR, grid, ComplexHeatmap, circlize Suggests: knitr, markdown, rmarkdown License: CeCILL | file 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tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter, lifecycle Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: 7465671632bf7aea25cf3bea95f0dc31 Package: SingleR Version: 2.14.1 Depends: SummarizedExperiment Imports: methods, Matrix, BiocGenerics, S4Vectors, DelayedArray, stats, utils, Rcpp, beachmat (>= 2.27.3) LinkingTo: Rcpp, beachmat, assorthead (>= 1.3.5) Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocParallel, SingleCellExperiment, scrapper (>= 1.5.16), scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: 2e09f942234181d484ca9c9a2425f9e6 Package: singscore Version: 1.32.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, 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License: GPL-2 MD5sum: 554fb19872847fb63573d5fd027c0acd Package: sitePath Version: 1.28.0 Depends: R (>= 4.2) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 16cd55153a71bd893b1cbc1673c27340 Package: sizepower Version: 1.82.0 Depends: stats License: LGPL MD5sum: 581c9234f807763b38bef21232fc5ab4 Package: sketchR Version: 1.8.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment, snifter, uwot, bluster, class License: MIT + file LICENSE MD5sum: 64de45c9a661c73f8e65be5e8fd372d5 Package: skewr Version: 1.44.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: fbe19147f416696dc60dfc35231544d5 Package: slingshot Version: 2.20.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 68f64f693e131f469236f8f03d192951 Package: SLqPCR Version: 1.78.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 9f748e25944a530fe9aa6d3f21d811f4 Package: SMAD Version: 1.28.0 Depends: R (>= 4.5.0) Imports: data.table, dplyr, magrittr (>= 1.5), Rcpp (>= 1.0.0), RcppAlgos, stats, tidyr, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 21f442f32d997655240259993212df7f Package: smartid Version: 1.8.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tibble, tidytext, UpSetR License: MIT + file LICENSE MD5sum: 51a96558124906ec613e71c54d340dd9 Package: SmartPhos Version: 1.2.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, SummarizedExperiment, data.table, shiny, shinythemes, shinyjs, shinyBS, shinyWidgets, parallel, DT, tools, stats, ggplot2, plotly, ggbeeswarm, pheatmap, grid, XML, MsCoreUtils, imputeLCMD, missForest, limma, proDA, decoupleR, piano, BiocParallel, doParallel, doRNG, e1071, magrittr, matrixStats, rlang, stringr, tibble, dplyr, tidyr, Biobase, vsn, factoextra, cowplot Suggests: knitr, BiocStyle, PhosR, testthat License: GPL-3 MD5sum: 9d7d3a4ca045f406fa3b0a1488fcc59d Package: SMITE Version: 1.40.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 6d012d9d48c9387614bc425350264b5a Package: smoothclust Version: 1.8.1 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: a984200a0bb1e5988c56e952a16fa495 Package: smoppix Version: 1.4.0 Depends: R (>= 4.5.0) Imports: spatstat.geom(>= 3.2.0),spatstat.random,methods,BiocParallel,SummarizedExperiment,SpatialExperiment,Rdpack,stats,utils,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),spatstat.model,openxlsx,Rfast,reformulas,mgcv LinkingTo: Rcpp Suggests: testthat,rmarkdown,knitr,DropletUtils,polyCub,RImageJROI,sp,ape,htmltools,funkycells,glmnet,doParallel License: GPL-2 MD5sum: 5ad2277a14ba75cba329e50a6ad8ac6a Package: SMTrackR Version: 1.0.0 Depends: R (>= 4.5) Imports: jsonlite, GenomicRanges, rtracklayer, stringr, BiocFileCache, S4Vectors Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 7e6adffa3aafec702b93b01bc5014dab Package: SNAGEE Version: 1.52.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 6dc982b2d932dff15adc1c25694579c3 Package: snapcount Version: 1.24.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: d8caf95c7718736029260206371fd487 Package: snifter Version: 1.22.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: a3f52130e34f12ffacadfa6750bc8cff Package: snm Version: 1.60.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 13019d8a17df0b078b77994ba1a1ccce Package: SNPediaR Version: 1.38.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 5e42b42e11303446df1b7c1dc0f33647 Package: SNPhood Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: 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SOMNiBUS Version: 1.20.0 Depends: R (>= 4.1.0) Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 84f17e116e761516c4944ca19600fd75 Package: sosta Version: 1.4.0 Depends: R (>= 4.4.0) Imports: terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, SingleCellExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel, EBImage, spatstat.random, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: ce79575e67e1132d944b58245c154f42 Package: SpaceMarkers Version: 2.2.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer, circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis Suggests: data.table, devtools, knitr, cowplot, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap Enhances: BiocParallel License: MIT + file LICENSE MD5sum: ca3f62274f813f7b5151ee316538fc24 Package: SpaceTrooper Version: 1.2.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, cowplot, glmnet, rhdf5, methods, rlang, SpatialExperimentIO Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), withr, viridis License: MIT + file LICENSE MD5sum: 93157583cfd4186bcf37a6a32d04cf3d Package: spacexr Version: 1.4.0 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: ce7253020d0adb7c1c281e828ec39c2a Package: Spaniel Version: 1.26.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: 6df84591809184df2ea67a9b000dd633 Package: SpaNorm Version: 1.6.0 Depends: R (>= 4.4) Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils, BiocParallel, BiocSingular Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce, ggnewscale, tensorflow License: GPL (>= 3) MD5sum: c34548b86881e7a9872f580e81fed603 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SparseSignatures Version: 2.22.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: fffb5583af88d212266c4ab93e63376e Package: spaSim Version: 1.14.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: fb5368146fbf6ed28b402d01d86b739e Package: SpatialArtifacts Version: 1.0.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, S4Vectors, scuttle, dplyr, terra, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BiocCheck, ggplot2, patchwork, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 49fccfda24e38df8704efa0a4b285a28 Package: SpatialCPie Version: 1.28.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 8417178f9aadb60af34d20bfeb1e54a6 Package: spatialDE Version: 1.18.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 38fdad8ea1714ec963eb91b81df71110 Package: SpatialDecon Version: 1.22.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: 8b5c8831b23927918415ab7a0154494b Package: SpatialExperiment Version: 1.22.0 Depends: R (>= 4.1.0), methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO License: GPL-3 MD5sum: 5bf6fe7d0468a56f8883ebb8804bdffd Package: SpatialExperimentIO Version: 1.4.0 Depends: R (>= 4.1.0) Imports: DropletUtils, SpatialExperiment, SingleCellExperiment, methods, data.table, arrow, purrr, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 2f8c8bb8fbf3f5496b48220f8cb01601 Package: spatialFDA Version: 1.4.0 Depends: R (>= 4.3.0) Imports: dplyr, ggplot2, parallel, patchwork, purrr, refund, SpatialExperiment, spatstat.explore, spatstat.geom, SummarizedExperiment, methods, stats, fda, tidyr, graphics, ExperimentHub, scales, S4Vectors, mgcv Suggests: stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: 47ae2b0c0d94ad6cda9e47211222c2b0 Package: SpatialFeatureExperiment Version: 1.14.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics (>= 0.51.2), BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, gmp, knitr, OSTA.data, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, VisiumIO, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: d8c5e52c07c59eef1a610a4992c362f5 Package: SpatialOmicsOverlay Version: 1.12.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 7bd33fc5d0309df837058dcda9f1b665 Package: spatialSimGP Version: 1.6.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: ccc3a2df094c6c74ad2491a353eb9e78 Package: speckle Version: 1.12.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 281aebb9bd202ce43dd6ba3793f6bb96 Package: specL Version: 1.46.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 687cb202ea5ff25b9b3fd655bd987f6f Package: SpeCond Version: 1.66.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 9484de37b3365ff493b12495e8fa6f02 Package: Spectra Version: 1.22.2 Depends: R (>= 4.1.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>= 1.23.6), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils, data.table Suggests: testthat, knitr (>= 1.1.0), MsDataHub, roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: ba4a05b9fbc3da4edac4275263d9ecc5 Package: SpectralTAD Version: 1.28.2 Depends: R (>= 3.6) Imports: dplyr, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: f66430a60ab7087e3463181d8c70f781 Package: SpectraQL Version: 1.6.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, MsDataHub, roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: 2e360b1faf092100290249378909bcc2 Package: SpectriPy Version: 1.2.1 Depends: R (>= 4.4.0), reticulate (>= 1.42.0) Imports: Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils, ProtGenerics, methods, data.table, snakecase Suggests: testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 67f5609f54894ab673473a4ab9b120be Package: SPEM Version: 1.52.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 02436b9e0bf1d716031b60d36e05aeb0 Package: SPIA Version: 2.64.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 3c36dbcdb469790e4e1806e32e1a89d4 Package: SPIAT Version: 1.14.0 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: ff7311019d57fcc7d9efa11d4a7738cc Package: SPICEY Version: 1.2.0 Depends: R (>= 4.5.0), utils, stats, grDevices Imports: GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors, ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 03f3e8bb31026e02fbfd3519c8779be9 Package: spicyR Version: 1.24.0 Depends: R (>= 4.1) Imports: BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, cli, concaveman, coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2, ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods, pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore, spatstat.geom, stats, survival, tibble, tidyr Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: fd3f56d9761ee0dbe467f3e874b5c982 Package: SpiecEasi Version: 2.0.0 Depends: R (>= 4.5.0), Imports: stats, methods, graphics, grDevices, huge (>= 1.3.2), pulsar (>= 0.3.11), MASS, VGAM, Matrix (>= 1.5), glmnet, phyloseq LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, boot, igraph, batchtools, testthat, covr, knitr, BiocStyle, rmarkdown, RefManageR, sessioninfo, magick License: GPL (>= 3) MD5sum: e9c838cbd40b7f34915a3dc5846d41f0 Package: spikeLI Version: 2.72.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 314a363c627f4c28e42fadd5fdf59d0f Package: spiky Version: 1.18.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: d8458790a60f9b78c11af5b15f44c5bc Package: spillR Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 4b85ac366c1995ebbb3c72864f3a2ba4 Package: spkTools Version: 1.68.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 3d553a61bc83a2887c52efd3244a8d90 Package: splatter Version: 1.36.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, lifecycle, locfit, matrixStats, methods, rlang, S4Vectors, scrapper, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave License: GPL-3 + file LICENSE MD5sum: fd8546e2eaf25478b56f1cd6f84cc7df Package: SpliceImpactR Version: 1.0.0 Depends: R (>= 3.5.0) Imports: data.table, BiocFileCache, BiocParallel, Biostrings, GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db, dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer, scales, stats, tidyr, tools, utils, magrittr, methods, S4Vectors Suggests: devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot, stringr, readr, tibble, BiocStyle, clusterProfiler, AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 5a76563bc0bd1b0bf7f7ab673718b13a Package: splicelogic Version: 1.0.1 Depends: R (>= 4.5.0) Imports: dplyr, magrittr, GenomicRanges, plyranges, tibble, IRanges, S4Vectors, rlang, methods, stats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), readr, wiggleplotr, GenomicFeatures, AnnotationHub, ggplot2, AnnotationDbi, Seqinfo License: MIT + file LICENSE MD5sum: dce25c98a4c3077f2e13ef32bf3453e4 Package: SpliceWiz Version: 1.14.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, h5mread, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: cdfe26f43854f2bf94d1acdbed13aa22 Package: SplicingFactory Version: 1.20.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 6a663aff70a13e0fb8fce13e621194fe Package: SplicingGraphs Version: 1.52.0 Depends: R (>= 3.5.0), GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), Seqinfo, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.refGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: dbe102bcf3fc3a3ab49d63bdfcadb3c3 Package: SplineDV Version: 1.4.0 Depends: R (>= 3.5.0) Imports: plotly, dplyr, scuttle, methods, Biobase, BiocGenerics, S4Vectors, sparseMatrixStats, SingleCellExperiment, SummarizedExperiment, Matrix (>= 1.6.4), utils Suggests: knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2, ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0) License: GPL-2 MD5sum: a753dfc400442e22d9f86736def1c184 Package: splineTimeR Version: 1.40.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: ea5e814eacb8df77cc731bb486cd677c Package: SPLINTER Version: 1.38.0 Depends: R (>= 3.6.0), grDevices, stats Imports: graphics, ggplot2, seqLogo, Biostrings, pwalign, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, Seqinfo, utils, plyr,stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis Suggests: txdbmaker, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: dc3f9e70546aac32199ba68586a4c1e3 Package: splots Version: 1.78.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: d3196ab6922d0dec7af2ad483b8c0d68 Package: SpNeigh Version: 1.0.0 Depends: R (>= 4.4.0) Imports: concaveman, dbscan, dplyr, FNN, ggplot2, limma, magrittr, Matrix, methods, patchwork, purrr, rlang, scales, Seurat, sf, SingleCellExperiment, SpatialExperiment, splines, stringr, SummarizedExperiment, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: d4fd22b54d5a29545ff3f05475d05392 Package: SPONGE Version: 1.34.1 Depends: R (>= 3.6) Imports: methods, Biobase, stats, ppcor, logger, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr, tibble Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: 50f221a966fa9e888fc23420ea28a9e3 Package: spoon Version: 1.8.0 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 38216f6aa2399d6f6009bd7f41ec1c22 Package: SpotClean Version: 1.14.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: e48d779470827f1e54e4e56be6373c70 Package: SPOTlight Version: 1.16.0 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, SingleCellExperiment, sparseMatrixStats, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: b4104259d4e3b223b13569ba31686631 Package: SpotSweeper Version: 1.8.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices, BiocParallel Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: aeae35a441d6b61ef4e5ea27844843b4 Package: spqn Version: 1.24.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: 358fb2107a14b897cd3930a01a80c972 Package: SPsimSeq Version: 1.22.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 MD5sum: d7f754abce73b5004b788fee34efa3d5 Package: squallms Version: 1.6.0 Depends: R (>= 4.1.0) Imports: xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5cfef605d0c1dce0af27869ac3cc19de Package: sRACIPE Version: 2.4.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics, doFuture, doRNG, future, foreach LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest License: MIT + file LICENSE MD5sum: 0ab27db81e8296ca46a5cc4c26d6cfb1 Package: SRAdb Version: 1.74.0 Depends: RSQLite, graph, RCurl Imports: R.utils Suggests: Rgraphviz License: Artistic-2.0 MD5sum: 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1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 84ecebbeb3c606b59556d33579c15645 Package: ssPATHS Version: 1.26.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 175532de090219c48172aec17a3020b4 Package: ssrch Version: 1.28.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: efb36022540899a22f42c36d39e76765 Package: ssviz Version: 1.46.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: 5f839d04b85254783176877bc44b6cdb Package: StabMap Version: 1.6.0 Depends: R (>= 4.4.0), Imports: igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel Suggests: scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats License: GPL-2 MD5sum: e361925f0ea246ff6455cc19b83a925c Package: STADyUM Version: 1.2.0 Depends: R (>= 4.5.0) Imports: GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr, ggplot2, progress, GenomeInfoDb, Rcpp, data.table, purrr, rtracklayer, tidyr, rlang, MASS LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: c2b42cfe0e7465ddef48b44612aaad4b Package: stageR Version: 1.34.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: 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foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: 0e2776a0243335f61046040cb2e3a627 Package: StatescopeR Version: 1.0.1 Depends: R (>= 4.5.0) Imports: S4Vectors, SummarizedExperiment, reticulate, methods, SingleCellExperiment, matrixStats, scran, basilisk, Matrix, ComplexHeatmap, ggplot2, cowplot, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, scRNAseq, scuttle, testthat License: MIT + file LICENSE MD5sum: bd93c38c388cf89c1b465bfb6d09c74b Package: Statial Version: 1.14.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR, edgeR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: 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SeuratObject, scPipe, shiny, SummarizedExperiment, SingleCellExperiment, SpatialExperiment, stats, umap, yaml LinkingTo: Rcpp, Rhdf5lib, testthat, Rhtslib Suggests: knitr, plotly, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 369bc9532a3cd8491072d093a25b7968 Package: strandCheckR Version: 1.30.0 Depends: ggplot2 (>= 4.0.0), Rsamtools, S4Vectors Imports: BiocGenerics, dplyr, Seqinfo, GenomicAlignments, GenomicRanges, gridExtra, IRanges, grid, methods, reshape2, rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene, tidyselect Suggests: BiocStyle, knitr, magrittr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 2f4ac52552b871a323b4b8bb4476eefe Package: STRINGdb Version: 2.24.0 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: dbb99e448dab2025305e464683a3c612 Package: struct Version: 1.24.0 Depends: R (>= 4.0) Imports: methods, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, httr2, jsonlite Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 MD5sum: 9cc4ce99ea486c7a230d8db0a05b9155 Package: Structstrings Version: 1.28.0 Depends: R (>= 4.0), S4Vectors (>= 0.47.2), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: ea644f1496e11a395a124ca1db823bfe Package: structToolbox Version: 1.24.0 Depends: R (>= 4.0), struct (>= 1.5.1) Imports: ggplot2, ggthemes, grid, gridExtra, httr, jsonlite, methods, scales, sp, stats, limma Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs License: GPL-3 MD5sum: 2af0fab711b6fd2630f1aacb2cc02998 Package: 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BiocParallel License: MIT + file LICENSE MD5sum: 62f3e77d5ab46d9d8df6829fc10c0522 Package: survcomp Version: 1.62.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: 8e2043e3e21103a9fdac52e56430b9c1 Package: survtype Version: 1.28.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5ea2e88210c8e4d6c84d945a9baddb04 Package: sva Version: 3.60.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: d5b9a7deaff4c928dcca31bf46c1c132 Package: svaNUMT Version: 1.18.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, 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prettydoc, broman, RSpectra, BiasedUrn, knitr, ks, igraph, testthat (>= 3.0.0), scuttle, magrittr, DropletUtils, tibble, tidyr, harmony, aplot, scales, ggsc, scatterpie, scran, scater, STexampleData, ape License: GPL-3 MD5sum: ec3744ab748d6fd9f496d76e09272a45 Package: SWATH2stats Version: 1.42.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods Suggests: testthat, knitr, rmarkdown Enhances: MSstats, PECA, aLFQ License: GPL-3 MD5sum: 7846bf96ab85e33d15bb47661e9946a5 Package: SwathXtend Version: 2.34.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: e44591d42a89baadf6f6db740ea5590c Package: swfdr Version: 1.38.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) MD5sum: 96ebedc688145d557102bd047b9f2aa7 Package: switchBox Version: 1.48.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 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DESeq2, DT, edgeR, gdata, ggplot2, glmnet, GSVA (>= 1.51.3), HGNChelper, magrittr, methods, pROC, RColorBrewer, reshape2, ROCit, S4Vectors, singscore, stats, SummarizedExperiment, tibble Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown, shiny, spelling, sva, testthat License: MIT + file LICENSE MD5sum: f94ab037e692017ff09cf4670f648505 Package: TCC Version: 1.52.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: f1df53e6804ab9d1810bf83179cbc97b Package: TCGAbiolinks Version: 2.40.0 Depends: R (>= 4.1.0) Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT License: GPL (>= 3) MD5sum: 930621de08cc3fbd29302e84207fa3f0 Package: TCGAutils Version: 1.32.2 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, glue, IRanges, methods, MultiAssayExperiment, RaggedExperiment, rvest, S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, Bioc.gff, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, miRNAmeConverter, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox, rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 1332020c651ce03e5df1cedee3560e34 Package: TCseq Version: 1.36.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: c8f4f33a45652bc7a1fa3e7944c3d26d Package: TDbasedUFE Version: 1.12.0 Imports: GenomicRanges, rTensor, readr, methods, MOFAdata, tximport, tximportData, graphics, stats, utils, shiny Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 936658ff19e1c9f869fbaea7b7d173d1 Package: TDbasedUFEadv Version: 1.12.1 Imports: TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods, graphics, stats, hash, shiny Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata, STRINGdb, enrichR, enrichplot, DOSE, gson, ggplot2 License: GPL-3 MD5sum: 1e2181a6927550d36e0d3938fbecab2b Package: TEKRABber Version: 1.16.0 Depends: R (>= 4.3) Imports: AnnotationHub, apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, GenomeInfoDb, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) License: LGPL (>= 3) MD5sum: e04e722d9e50002b0f59e27982dfd2d2 Package: TENET Version: 1.4.0 Depends: R (>= 4.5) Imports: graphics, grDevices, stats, utils, tools, S4Vectors, GenomicRanges, IRanges, parallel, pastecs, ggplot2 (>= 4.0), RCircos, survival, BSgenome.Hsapiens.UCSC.hg38, seqLogo, Biostrings, matlab, TCGAbiolinks, methods, R.utils, MultiAssayExperiment, SummarizedExperiment, sesame, sesameData, AnnotationHub, ExperimentHub, TENET.ExperimentHub, rtracklayer, MotifDb, BAMMtools, survminer Suggests: TENET.AnnotationHub, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: e2b5a88c819ca956ff71119a355fc99a Package: TENxIO Version: 1.14.0 Depends: R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment Imports: BiocBaseUtils, BiocGenerics, BiocIO, Seqinfo, GenomicRanges, HDF5Array, Matrix, MatrixGenerics, methods, readr, rhdf5, R.utils, S4Vectors, utils Suggests: BiocStyle, DropletTestFiles, ExperimentHub, knitr, RaggedExperiment (>= 1.33.3), rmarkdown, Rsamtools, tinytest License: Artistic-2.0 MD5sum: 77fa645fa8be5a42e27c87646dcb9a8a Package: tenXplore Version: 1.34.0 Depends: R (>= 4.0), shiny Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils, BiocFileCache Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 2cfb3b265548e91a6ff7d5a447f9182e Package: TEQC Version: 4.34.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: S4Vectors, Seqinfo, GenomicRanges, Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: fda546ace9bf19a1b26fe9206d5a1e04 Package: terapadog Version: 1.4.0 Imports: DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets, biomaRt, methods Suggests: apeglm, BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: d4ba0384f377815f464b3ac0fc639aad Package: ternarynet Version: 1.56.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 5dcb10cd768d451dc32b410bc3dfaf6b Package: terraTCGAdata Version: 1.16.0 Depends: AnVILGCP, MultiAssayExperiment Imports: AnVIL, BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: AnVILBase, GCPtools, knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6b39a7b7dfc37b21a8ea049a5afe5f90 Package: TFARM Version: 1.34.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots 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ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, S4Vectors, Seqinfo, meta, plotly, scales, tidyr, purrr, tibble, ggplot2, DESeq2, edgeR, limma, babelgene, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, RColorBrewer, RUnit, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 65b3d457563e36ed7a08cdce0e2b10e4 Package: TFHAZ Version: 1.34.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2c2f4d9bb5a812af5d7fe8fdaf67c8fb Package: TFutils Version: 1.32.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, Seqinfo, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 3464fab88b8d51f369967ddc0408a245 Package: tidybulk Version: 2.2.0 Depends: R (>= 4.4.0), ttservice (>= 0.3.6) Imports: tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang, purrr, tidyselect, stats, parallel, utils, lifecycle, scales, ggplot2, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, fastmatch, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway License: GPL-3 MD5sum: 88915a1227e25912bc0267360e8b16d3 Package: tidyCoverage Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, tibble, ggplot2, ggrastr, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, TxDb.Mmusculus.UCSC.mm10.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f4a1084e0b350cfd91f55e06df377d1a Package: tidyexposomics Version: 1.0.0 Depends: R (>= 4.5.0), MultiAssayExperiment Imports: BiocFileCache, broom, cluster, dplyr, DT, factoextra, fenr, ggplot2 (>= 3.4.0), ggpubr, ggrepel, Hmisc, httr, igraph, jsonlite, limma, MASS, methods, mixOmics, naniar, purrr, readr, RGCCA, rlang, S4Vectors, scales, shiny, stats, stringr, SummarizedExperiment, tibble, tidybulk, tidyr, utils Suggests: BiocStyle, circlize, curl, densityClust, DiagrammeR, dynamicTreeCut, edgeR, forcats, ggh4x, ggnewscale, ggraph, ggridges, ggsci, ggvenn, grid, gridExtra, impute, janitor, knitr, matrixStats, mice, mirt, missForest, MOFA2, nipalsMCIA, openxlsx, patchwork, reticulate, rmarkdown, testthat (>= 3.0.0), tidygraph, tidyHeatmap, tidytext, tidyverse License: MIT + file LICENSE MD5sum: 2d76e89f549a9f5b97dbfed65770fdd3 Package: tidyFlowCore Version: 1.6.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a049ae93cf083a452994fc1d70ed9e32 Package: tidyomics Version: 1.8.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidySpatialExperiment, tidyseurat, plyranges, purrr, rlang, stringr, cli, Suggests: utils, tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 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fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly, rbibutils, prettydoc License: GPL-3 MD5sum: cf7715c3ae2fc0e6c321f141c4c066f6 Package: tidySpatialExperiment Version: 1.8.0 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment, ttservice Imports: SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2 (>= 4.0.0), plotly, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick, tidygate (>= 1.0.13), shiny Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment License: GPL (>= 3) MD5sum: 6ba7472494334ade2c65e5060ea83787 Package: tidySummarizedExperiment Version: 1.22.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.5.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig, plyxp Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, plotly, rbibutils, prettydoc, airway License: GPL-3 MD5sum: 89c5678d89cf6259d2de8b0c6cf05aeb Package: tigre Version: 1.66.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: 23a2149e738a138073a91e435aebad52 Package: TileDBArray Version: 1.22.0 Depends: SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7) Imports: methods, tiledb, S4Vectors Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 1e8041218abf6d33d48788815f79781b Package: tilingArray Version: 1.90.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 107e4dbcdbca9ede1c89fc451abb070b Package: timecourse Version: 1.84.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 964bdb9a657d8f63106f80f3d5ffd4fe Package: timeOmics Version: 1.24.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 519ef2398c5e5862e0109f8330d91a9f Package: timescape Version: 1.36.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 1ed01e5938c5ac4c52f5c42848e5c5e9 Package: TIN Version: 1.44.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 3a1a7f0a1dcd1fddf51d2fa3ceeea98f Package: TissueEnrich Version: 1.32.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8ee14e11ac71d8f4229283142257d1c5 Package: tkWidgets Version: 1.90.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: c6a5ab5050be9cb4e0a583107a840f90 Package: tLOH Version: 1.19.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0e53f0da21a724af39c521c5fcd65c51 Package: TMixClust Version: 1.34.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: eaa21d0d66ac5786f9b31f9dca1be3cf Package: TMSig Version: 1.6.0 Depends: R (>= 4.4.0), limma Imports: circlize, ComplexHeatmap, data.table, grDevices, grid, GSEABase, Matrix, methods, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: e521835fe3263ef0a266f638b0ef0f0e Package: TnT Version: 1.34.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: ae59123ed6b37560fa0ef1aa30dea4dd Package: TOAST Version: 1.26.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: 0e8026a9583f71fe43ab37fae552da96 Package: tomoda Version: 1.22.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 636dd28d7e02f9c2eb1edd477adbd0ff Package: tomoseqr Version: 1.16.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a3d21bc8e4ff07d4dd9ace9cc2d5daa3 Package: TOP Version: 1.12.0 Depends: R (>= 4.1.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: ae0fd8eb8255c70e7fb4ae2cd5712723 Package: topconfects Version: 1.28.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: 4c1d10ca43ce8611528c66e27334f3bc Package: topdownr Version: 1.34.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 8292215c905863465783fdf0308f13e0 Package: topGO Version: 2.64.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, multtest, Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown License: LGPL MD5sum: 63f7763de85a66bffa2ec683e9a311ae Package: ToxicoGx Version: 2.16.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: 294a8fcadc9219745274b6e134b21576 Package: TPP Version: 3.40.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rlang, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 75197eccb6be8d5e3b0b5fbbdc7e596d Package: TPP2D Version: 1.28.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2aa14c2303b65887963762b4af871b9c Package: tpSVG Version: 1.8.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6bbf301cb40d2ec1881077b2ee22697a Package: tracktables Version: 1.46.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 9a3fa4b510527109a857791a586bfb8e Package: trackViewer Version: 1.48.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 50d98bc8dfedb6a4b6bee2a0a3eb3559 Package: tradeSeq Version: 1.26.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 0b89cec7ccf9e847b83f371de9cd1498 Package: TrajectoryGeometry Version: 1.20.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: a233a75813803e9e5bd09e595e28af67 Package: TrajectoryUtils Version: 1.20.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 68a121ddf784527a11f67059fd9f6673 Package: transcriptogramer Version: 1.34.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: b4aa00d64d970152602dfa388577876c Package: transcriptR Version: 1.40.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat, e1071 License: GPL-3 MD5sum: cd7bd546a8901930afbbdacf9dfd2fc3 Package: transformGamPoi Version: 1.18.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 71d248cc4459e451e207e3c95c9633ad Package: tRanslatome Version: 1.50.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 576d3be11fd056e586b5c4fde17e1ba2 Package: transmogR Version: 1.8.1 Depends: R (>= 4.1.0), Biostrings, GenomicRanges Imports: BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0) License: GPL-3 MD5sum: 39568d969cb63015227db013b24d2d66 Package: transomics2cytoscape Version: 1.22.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: d8e653155a876a7c7b803c8104780d1a Package: traseR Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 0a0646daf501520faff7f6b1eebe972b Package: TreeAndLeaf Version: 1.24.0 Depends: R(>= 4.4) Imports: RedeR(>= 3.6.1), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: 43c408150d78e25c338fe4e8e91326fa Package: treeclimbR Version: 1.8.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle, GenomeInfoDb License: Artistic-2.0 MD5sum: ff532cc8169f1c144241e526efe8a377 Package: treeio Version: 1.36.1 Depends: R (>= 4.1.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 316404e6706f6dbeb9da7ce13e319489 Package: treekoR Version: 1.20.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: dfc51a16b34c1b565a263be00d88c028 Package: TreeSummarizedExperiment Version: 2.20.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 3474b2c314ef5e53664a5f8cae1922c0 Package: TREG Version: 1.16.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: b7042a917d81652ce23bf171e433d85c Package: Trendy Version: 1.34.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 39138434b42ec2c6cc756c38b0936e1b Package: TRESS Version: 1.18.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 4352c10a063de668de10b461e6bf7dad Package: tricycle Version: 1.20.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: fa7a6fdc50c75474878d9fc137155842 Package: TrIdent Version: 1.4.0 Depends: R (>= 4.2.0) Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: GPL-2 MD5sum: 10f32ea9ac325b3ae342c0d40f6bb3d4 Package: trio Version: 3.50.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1), data.table Suggests: mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 5e261e797b485bc1daf4f2b9310beba3 Package: triplex Version: 1.52.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 5a074557fc6550c7f6e3ea4756d8b581 Package: tripr Version: 1.18.0 Depends: R (>= 4.1.0), shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis Enhances: parallel License: MIT + file LICENSE MD5sum: f815e578a6b7ca2c1b7311979c193302 Package: tRNA Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 2c0751ee9138050b6ee273434b8bebac Package: tRNAdbImport Version: 1.30.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 741397acc403b6b4108ee903345e598b Package: tRNAscanImport Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, Seqinfo, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 782bdd27df825d8c7964918f18e4ca0f Package: TRONCO Version: 2.44.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 873cba3f7724a95eb8c3b7577223fc19 Package: TSAR Version: 1.10.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 9cfde1e5822405fa9a3ab585d4df6ace Package: TSCAN Version: 1.50.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: ccf3f7bdecb91d221477cf0bf22437cf Package: ttgsea Version: 1.20.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 8981c6a82ddc7f583daef33e92df3485 Package: TTMap Version: 1.34.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 285d60fe081bdd0d05ba86836b3d663d Package: TurboNorm Version: 1.60.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 5fe27f589619eb0fa026a12cf481a25a Package: TVTB Version: 1.38.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, Seqinfo, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 6c937b645402b99244e980487f91a7ed Package: tweeDEseq Version: 1.58.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: c6c67046a5bb1d8446538b5d8282b2a3 Package: twilight Version: 1.88.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, splines, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 2becea7999aa3488e8a869c5313413ec Package: twoddpcr Version: 1.36.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 3ddfb5777033a79a229c94ead43688c6 Package: txcutr Version: 1.18.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3, GenomeInfoDbData License: GPL-3 MD5sum: 813fb982ad87a66a9e70ac74d84693c2 Package: txdbmaker Version: 1.7.3 Depends: BiocGenerics, S4Vectors (>= 0.47.6), Seqinfo, GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4) Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils (>= 1.7.1), GenomeInfoDb, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: c25548696a8801dcd0bf3068fe1c56d5 Package: tximeta Version: 1.30.0 Depends: R (>= 4.1.0) Imports: SummarizedExperiment (>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi, DBI, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.37.5), org.Dm.eg.db, DESeq2, edgeR (>= 4.9.2), limma, devtools, macrophage License: GPL-2 MD5sum: 29cdfec44eed435dc2babce4f7e8c960 Package: tximport Version: 1.40.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR (>= 4.9.2), DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 9ed4cfdb2d545726da3d23e45d4d2329 Package: UCell Version: 2.16.0 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 655693831510f6638ba60de5da5e2a4f Package: UCSC.utils Version: 1.7.1 Imports: methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6) Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0846737f96ab387581ea665bf9eee852 Package: Ularcirc Version: 1.30.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, moments, Organism.dplyr, plotgardener,R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 48f26533e1b3f092e2c3372df3f5c13f Package: UMI4Cats Version: 1.22.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: c733ab9bc854f397f18220813dcbae4c Package: uncoverappLib Version: 1.22.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 8db5590c0340bf8e7db6232b41c65499 Package: UNDO Version: 1.54.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 89a91f244a4b11126b703a9f9c7f3d34 Package: unifiedWMWqPCR Version: 1.48.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: 8ed4473371a3ea6af2917813ce468861 Package: UniProt.ws Version: 2.52.1 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics, httr2, jsonlite, methods, progress, rjsoncons, rlang, utils Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: a9864306777cfb00d79d5178394827f7 Package: Uniquorn Version: 2.32.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: 5ffecb52b76938bfb6f5e80e6dd1f92c Package: universalmotif Version: 1.30.1 Depends: R (>= 4.1.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 4b7238657af60a4c602258dedf6a35e6 Package: updateObject Version: 1.16.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: cffd84c99aceecfdeb7380430956ac67 Package: UPDhmm Version: 1.8.0 Depends: R (>= 4.1.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, stats, BiocParallel, GenomeInfoDb Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr, BiocManager License: MIT + file LICENSE MD5sum: 37ac2d669b51fe33e283f05d2c061bdf Package: uSORT Version: 1.38.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 271feb24b97ce546bcbf802ccd359e7f Package: VAExprs Version: 1.18.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: b837de1583e7ced92affaa4a6e42b299 Package: VanillaICE Version: 1.74.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: c30002371142abf8d2e6d2b05bbe19b5 Package: VarCon Version: 1.20.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: aa8ababd288bdc06f873545d622b03ce Package: variancePartition Version: 1.42.0 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, reformulas, matrixStats, RhpcBLASctl, reformulas, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 2.0-1), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 4386ac166cb191b9e87a1a612871366d Package: VariantAnnotation Version: 1.58.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1) Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4), curl LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: e6bc8621319b72e04268e6997f4750d7 Package: VariantFiltering Version: 1.48.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 22166eebdb79b2bf77928c693578e1c4 Package: VariantTools Version: 1.54.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: 8dacedb9c2d81a91ca0230b80c4f752c Package: VaSP Version: 1.24.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 9cc5e8b7581f2ef2761c6ecb00622809 Package: vbmp Version: 1.80.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 674d2e7cbc31fbf8b99313905c874abf Package: VCFArray Version: 1.28.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: e5ab53f0874af46b7e5963f6e617cba8 Package: VDJdive Version: 1.14.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: ebbc5eaca2cbd946fabca2214c9206b9 Package: VegaMC Version: 3.50.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: f2f8f61a9c1edae6a4cc74a137ad671c Package: velociraptor Version: 1.22.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: 23ca9cc8c6703c0822741949e632ead4 Package: veloviz Version: 1.18.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 975f7912035b9690c4b8cf6993056838 Package: VennDetail Version: 1.28.0 Depends: R (>= 4.0.0) Imports: dplyr, DT, ggplot2, grid, gridExtra, magrittr, methods, patchwork, plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0), markdown, RColorBrewer, rstudioapi License: GPL-2 MD5sum: 29bbb262b88c1ec5d3ef15b8e8be4bba Package: VERSO Version: 1.22.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 77773898fdff32846a4c8b1315159eda Package: vidger Version: 1.32.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: 452185be3cf9058f2f196e1b5f82ebac Package: viper Version: 1.46.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: cd151bfaaaa3776833e93da003ded1b4 Package: ViSEAGO Version: 1.26.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut, GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT, DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea, ggplot2, htmlwidgets, igraph, methods, plotly, scales, ComplexHeatmap, circlize Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager, stats, utils, grDevices, processx License: GPL-3 MD5sum: 8a513a65a399631551bbd238e55b93fb Package: VisiumIO Version: 1.8.0 Depends: R (>= 4.5.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 150a6afcc66a42adfd696b59d4750f11 Package: visiumStitched Version: 1.4.0 Depends: R (>= 4.4), SpatialExperiment Imports: BiocBaseUtils, BiocGenerics, clue, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e0d9c39d4872750640e01db68f12934d Package: vissE Version: 1.20.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: d7c5a5d61d39bce071eb30952f44c62e Package: VISTA Version: 1.0.0 Depends: R (>= 4.3) Imports: AnnotationDbi, cli, clusterProfiler, colorspace, DESeq2, dplyr, edgeR, forcats, ggplot2, ggrepel, GGally, ggpubr, grid, matrixStats, methods, msigdbr, limma, purrr, rlang, S4Vectors, scales, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, viridis Suggests: airway, BiocStyle, circlize, ComplexHeatmap, DT, EnhancedVolcano, ggpointdensity, ggridges, ggalluvial, ggcorrplot, ggrain, ggvenn, enrichplot, knitr, magrittr, patchwork, org.Hs.eg.db, org.Mm.eg.db, quarto, rmarkdown, yaml, writexl, testthat (>= 3.0.0), uwot, xCell2 License: GPL-3 MD5sum: d107fe244d7bdcb2c0cccedef721f7d0 Package: vmrseq Version: 1.4.0 Depends: R (>= 4.5.0) Imports: bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges, ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab, HDF5Array, data.table, SummarizedExperiment, IRanges, S4Vectors, devtools Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 177b5eb62b4a3d48a5a9ef15c3d0a673 Package: Voyager Version: 1.14.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, biscale, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 4f2419907740d05bc6492d8728ad5970 Package: VplotR Version: 1.22.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, Seqinfo, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: 450e9443ff7b5163b34b5ffaa1571c47 Package: vsclust Version: 1.14.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr, magick License: GPL-2 MD5sum: 4426e5549c51d9bf2ba5637eb3ddcc26 Package: vsn Version: 3.80.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat, hexbin License: Artistic-2.0 MD5sum: 75c6e5d7f7164375004130b629cb0549 Package: vtpnet Version: 0.52.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 4645f85a8058093bb5057da009c5b875 Package: vulcan Version: 1.34.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 8f933375b65eb1a06e697a5645d3c4dd Package: wateRmelon Version: 2.18.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 8a395c3484cbb787e8e26833a452446e Package: wavClusteR Version: 2.46.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr, txdbmaker Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: f58058050504d4a4d2e7eccb1558243b Package: wavFeatExt Version: 1.0.0 Depends: R (>= 4.5) Imports: DNAcopy, wavethresh, MASS, randomForest, glmnet, pROC, neuralnet, e1071, class, caret, ica, stats, graphics, utils, pls, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 657df60bdfbe9e3593a5179db77b0c02 Package: weaver Version: 1.78.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 7e35ed2790c8c1480f2ef256d356c3c2 Package: webbioc Version: 1.84.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: cd0de0967effb72e8617fe94fd6097f7 Package: weitrix Version: 1.24.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: b3f0ea8361947c1b78fe8e65caa637e8 Package: widgetTools Version: 1.90.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: d73e334012241478bed5a32ac799b89a Package: wiggleplotr Version: 1.36.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter, arrow License: Apache License 2.0 MD5sum: 4ca6d3b8ee287b41f314008bb12e03e6 Package: wpm Version: 1.22.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e0ec5aa4b4ab68fe8256751660094aaa Package: wppi Version: 1.20.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: d0729344ee8a1909cdd25a5fdef361bd Package: Wrench Version: 1.30.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 68d6df7a47009feb8c0408ed2724913c Package: XAItest Version: 1.4.0 Depends: R (>= 3.5.0) Imports: limma, randomForest, kernelshap, caret, lime, DT, methods, SummarizedExperiment, ggplot2 Suggests: knitr, ggforce, shapr (>= 1.0.1), airway, xgboost, BiocGenerics, RUnit, S4Vectors License: MIT + file LICENSE MD5sum: 4a13e135891a6c0bfae9e6312422e59f Package: xCell2 Version: 1.4.0 Depends: R (>= 4.0.0) Imports: SummarizedExperiment, SingleCellExperiment, Rfast, singscore, AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel, Matrix, minpack.lm, pracma, methods, readr, magrittr, progress, quadprog Suggests: testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr, EnhancedVolcano, BiocStyle License: GPL (>= 3) MD5sum: fb3621381b2a95c66a25aab3738f1a8a Package: xcms Version: 4.10.1 Depends: R (>= 4.1.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.21.5), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv, rhdf5, MsDataHub (>= 1.11.2) Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: 317d9944a547a6af8d33c61dfb0c9ccb Package: xcore Version: 1.16.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: f4d503b4d839ad9248a8df1b042c322e Package: XDE Version: 2.58.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: 5ab6939b033d5c6036d40f4045aa6cf1 Package: XeniumIO Version: 1.4.0 Depends: TENxIO, R (>= 4.5.0) Imports: BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, VisiumIO (>= 1.7.5) Suggests: arrow, BiocFileCache, BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 25a38e567051b5e2306762ef2e1380f2 Package: xenLite Version: 1.6.0 Depends: R (>= 4.1) Imports: SpatialExperiment, BiocFileCache, Matrix, S4Vectors, SummarizedExperiment, methods, utils, EBImage, shiny, HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr, graphics, stats Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff License: Artistic-2.0 MD5sum: 18ca99fcd5ce004780d2897c68ea623b Package: Xeva Version: 1.28.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 4fc81e1fb9e8696dbad8c42ded55bd50 Package: XINA Version: 1.30.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 1eb7305fca89c1ebba9276260afd14b9 Package: xmapbridge Version: 1.70.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 806539ce81325224470b12b7ff57b7b2 Package: XVector Version: 0.52.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.43.8) Imports: methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 23865ec47cd4f4d22a672d8d47a8c101 Package: yamss Version: 1.38.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: d2e1e2f8dba0b288ab554d200c0f287f Package: YAPSA Version: 1.38.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, Seqinfo, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f4e5f2f3abe78e1a29aaee4086c7335a Package: yarn Version: 1.38.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 65f478ab3b4c0786547c4d221082310f Package: zellkonverter Version: 1.22.0 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SparseArray, SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, SpatialExperiment, spelling, testthat, withr License: MIT + file LICENSE MD5sum: ccf44e75373cca0b071e76dfd2c98ed5 Package: zenith Version: 1.14.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 2bad959fe2b887eb36cc8dbbaf18fef7 Package: zFPKM Version: 1.34.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: df10d352620b467c5ef5a93f7efc5b1d Package: zinbwave Version: 1.34.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: c3e2baf6006576d23d78a5f245103bb5 Package: zitools Version: 1.6.0 Depends: R (>= 4.4.0), methods Imports: phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome License: BSD_3_clause + file LICENSE MD5sum: bfc6fc8e171dbe59726831f16819c6e6 Package: ZygosityPredictor Version: 1.12.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: ea985f1a2a35976462c423b264c267ca