DOI: 10.18129/B9.bioc.recount    

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

Explore and download data from the recount project

Bioconductor version: Development (3.15)

Explore and download data from the recount project available at Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at

Author: Leonardo Collado-Torres <lcolladotor at>, Abhinav Nellore <anellore at>, Andrew Jaffe <andrew.jaffe at>, E. Taub <mtaub at>, Margaret Kammers <kai.kammers at>, A. Ellis <sellis18 at>, Kai Hansen <kasperdanielhansen at>, Shannon Langmead <langmea at>, E. Leek <jtleek at>, Kasper Collado-Torres <lcolladotor at>, Daniel Nellore <anellore at>, Ben Jaffe <andrew.jaffe at>, Jeffrey Taub <mtaub at>, T. Kammers <kai.kammers at>

Maintainer: Leonardo Collado-Torres <lcolladotor at>

Citation (from within R, enter citation("recount")):


To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel


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


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biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.4 (R-3.3) (5 years)
License Artistic-2.0
Depends R (>= 3.3.0), SummarizedExperiment
Imports BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.35.3), S4Vectors, stats, utils
Suggests AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6),, RefManageR, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer
Depends On Me
Imports Me psichomics, recountWorkflow, RNAAgeCalc
Suggests Me dasper, ODER, recount3
Links To Me
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