scRNAseq
This is the development version of scRNAseq; for the stable release version, see scRNAseq.
Collection of Public Single-Cell RNA-Seq Datasets
Bioconductor version: Development (3.24)
Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.
Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("scRNAseq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scRNAseq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scRNAseq")| User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData, SingleCellData |
| Version | 2.27.0 |
| License | CC0 |
| Depends | SingleCellExperiment |
| Imports | utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub(>= 2.3.4), AnnotationHub(>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | OSCA.basic, OSCA.intro, OSCA.workflows, scrapbook, SingleRBook |
| Imports Me | singleCellTK, OSTA |
| Suggests Me | APL, augere.solo, BASiCS, batchelor, bluster, ccImpute, CellMentor, ClusterFoldSimilarity, Coralysis, CSOA, destiny, dittoSeq, Glimma, hammers, iSEE, iSEEfier, iSEEhex, iSEEid, iSEEindex, iSEEu, looking4clusters, miloR, miQC, mumosa, ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scECODA, scFeatureFilter, scLang, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, StatescopeR, UCell, velociraptor, zellkonverter, zinbwave, LISTO, speakeasyR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scRNAseq_2.27.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scRNAseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scRNAseq |
| Package Short Url | https://bioconductor.org/packages/scRNAseq/ |
| Package Downloads Report | Download Stats |