recount
This is the released version of recount; for the devel version, see recount.
All Bioconductor versions of recount
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
Explore and download data from the recount project
Bioconductor version: 3.23 · Package version: 1.38.0
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. 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 http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
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 gmail.com>
Citation
From within R, enter citation("recount"):
Leonardo Collado-Torres, Jeffrey T. Leek. recount: Explore and download data from the recount project. doi:10.18129/B9.bioc.recount, R package version 1.38.0, https://bioconductor.org/packages/recount.
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")
BiocManager::install("recount")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.38.0 |
| License | Artistic-2.0 |
| URL | https://github.com/leekgroup/recount |
| Bug Reports | https://support.bioconductor.org/t/recount/ |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 years) |
| Downloads rank | 329 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/recount/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("recount")| Basic DESeq2 results exploration | HTML | R Script |
| recount quick start guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | recount_1.38.0.tar.gz |
| Windows binary (x86_64) | recount_1.37.0.zip |
| macOS binary (arm64) | recount_1.38.0.tgz |
| macOS binary (x86_64) | recount_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/recount |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/recount |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5.0), 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, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer
Reverse dependencies
Imports Me (4): psichomics, recountWorkflow, RNAAgeCalc, RnaSeqSampleSize
Suggests Me (1): recount3