scRNAseq

This is the development version of scRNAseq; for the stable release version, see scRNAseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

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

Davide Risso, Michael Cole. scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets. doi:10.18129/B9.bioc.scRNAseq, R package version 2.27.0, https://bioconductor.org/packages/scRNAseq.

Generated from the package metadata; it may differ from the package's own citation.

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SequencingData, SingleCellData
Version	2.27.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
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

Suggests	BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager
Linking To
Enhances
Depends On Me	OSCA.advanced, OSCA.intro, OSCA.workflows, scrapbook, SingleRBook
Imports Me	OSTA, singleCellTK
Suggests Me	APL, augere.solo, BASiCS, batchelor, BiocDuckDB, bluster, ccImpute, CellMentor, ClusterFoldSimilarity, Coralysis, CSOA, destiny, dittoSeq, Glimma, GSABenchmark, hammers, iSEE, iSEEfier, iSEEhex, iSEEid, iSEEindex, iSEEu, LISTO, looking4clusters, miloR, miQC, mumosa, ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scECODA, scFeatureFilter, scLang, scone, scran, scrapper, scStability, scTreeViz, scuttle, SingleCellExperiment, SingleR, speakeasyR, SplineDV, StatescopeR, UCell, velociraptor, zellkonverter, zinbwave
Links To Me
Build Report	Build Report, r-universe

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