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Collection of Public Single-Cell RNA-Seq Datasets

Bioconductor version: Release (3.18)

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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

User's Guide HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData, SingleCellData
Version 2.16.0
License CC0
Depends SingleCellExperiment
Imports utils, methods, BiocGenerics, S4Vectors, GenomicRanges, SummarizedExperiment, ExperimentHub(>= 2.3.4), AnnotationHub(>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools
Linking To
Depends On Me OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.workflows, SingleRBook
Imports Me singleCellTK
Suggests Me APL, BASiCS, batchelor, bluster, ccImpute, 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
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Package Archives

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

Source Package scRNAseq_2.16.0.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/
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