DOI: 10.18129/B9.bioc.recount    

Explore and download data from the recount project

Bioconductor version: Release (3.6)

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 <lcollado at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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


biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.4.6
In Bioconductor since BioC 3.4 (R-3.3) (1.5 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, BiocStyle(>= 2.5.19), DESeq2, devtools (>= 1.6), EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6),, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat
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Source Package recount_1.4.6.tar.gz
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