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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 (3.19)

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 (from within R, enter citation("scRNAseq")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData, SingleCellData
Version 2.17.0
License CC0
Depends SingleCellExperiment
Imports utils, methods, BiocGenerics, S4Vectors, GenomicRanges, SummarizedExperiment, ExperimentHub(>= 2.3.4), AnnotationHub(>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures
System Requirements
URL
See More
Suggests BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools
Linking To
Enhances
Depends On Me OSCA.basic, OSCA.intro, OSCA.workflows, SingleRBook
Imports Me singleCellTK
Suggests Me APL, BASiCS, batchelor, bluster, ccImpute, ClusterFoldSimilarity, destiny, dittoSeq, Glimma, iSEE, iSEEhex, iSEEu, miQC, mumosa, scAnnotatR, scater, scDblFinder, scFeatureFilter, scone, scran, scTreeViz, scuttle, SingleCellExperiment, SingleR, SummarizedBenchmark, UCell, velociraptor, zellkonverter, zinbwave
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scRNAseq_2.17.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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