Package: CNEr
Version: 1.45.2
Date: 2024-04-23
Title: CNE Detection and Visualization
Description: Large-scale identification and advanced visualization 
             of sets of conserved noncoding elements.
Author: Ge Tan <ge_tan@live.com>
Maintainer: Boris Lenhard <b.lenhard@imperial.ac.uk> Damir Baranasic <damir.baranasic@lms.mrc.ac.uk>
Imports: Biostrings (>= 2.33.4), pwalign, DBI (>= 0.7), RSQLite (>=
        0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16),
        Seqinfo (>= 0.99.2), rtracklayer (>= 1.25.5), XVector (>=
        0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>=
        0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics,
        tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0),
        poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0),
        R.utils (>= 2.3.0), KEGGREST (>= 1.14.0)
Depends: R (>= 3.5.0)
Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,
        BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
        TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Ggallus.UCSC.galGal3
LinkingTo: S4Vectors, IRanges, XVector
VignetteBuilder: knitr
License: GPL-2 | file LICENSE
License_restricts_use: yes
URL: https://github.com/ComputationalRegulatoryGenomicsICL/CNEr
BugReports: https://github.com/ge11232002/CNEr/issues
Type: Package
biocViews: GeneRegulation, Visualization, DataImport
NeedsCompilation: yes
LazyData: no
Collate: GRangePairs-class.R GRangePairs-methods.R Axt-class.R
        CNE-class.R utils.R ceScan.R plot.R makeGeneDbFromUCSC.R
        IO-methods.R scoringMatrix.R subAxt-methods.R Axt-methods.R
        DB.R AssemblyStats.R GRB.R WholeGenomeAlignment.R Ancora.R
        CNE-methods.R GO.R KEGG.R
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: devel
git_last_commit: a1ee436
git_last_commit_date: 2025-08-05
Repository: Bioconductor 3.22
Date/Publication: 2025-08-05
Packaged: 2025-08-05 22:08:41 UTC; biocbuild
Built: R 4.5.1; x86_64-w64-mingw32; 2025-08-06 12:56:19 UTC; windows
Archs: x64
