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Explore and download data from the recount project

Bioconductor version: Release (3.19)

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 [aut, cre] , Abhinav Nellore [ctb], Andrew E. Jaffe [ctb] , Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb] , Kasper Daniel Hansen [ctb] , Ben Langmead [ctb] , Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcolladotor at>

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


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

Basic DESeq2 results exploration HTML R Script
recount quick start guide HTML R Script
Reference Manual PDF


biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.30.2
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), SummarizedExperiment
Imports BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.35.3), S4Vectors, stats, utils
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Suggests AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6),, RefManageR, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer
Linking To
Depends On Me
Imports Me psichomics, RNAAgeCalc, recountWorkflow
Suggests Me recount3
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package recount_1.30.2.tar.gz
Windows Binary
macOS Binary (x86_64) recount_1.30.2.tgz
macOS Binary (arm64) recount_1.30.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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