recount – A large-scale resource of analysis-ready RNA-seq expression data

recount is a resource of processed and summarized expression data spanning nearly 60,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associated recount Bioconductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed study consists of meta/phenotype data, the expression levels of genes and their underlying exons and splice junctions, and corresponding genomic annotation. The developers also provide data summarization types for quantifying novel transcribed sequence including base-resolution coverage and potentially unannotated splice junctions. They present workflows illustrating how to use recount to perform differential expression analysis including meta-analysis, annotation-free base-level analysis, and replication of smaller studies using data from larger studies. recount provides a valuable and user-friendly resource of processed RNA-seq datasets to draw additional biological insights from existing public data.


Availability – The resource is available at

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Andrew E Jaffe AE, Ben Langmead B, Jeffrey Leek J. (2016) recount: A large-scale resource of analysis-ready RNA-seq expression data. bioRXiv [Epub ahead of print]. [abstract]

One comment

  1. Hi,

    I would just like to point out that the recount R package is now available via Bioconductor 3.4 (currently Bioc-devel) at

    If you need support with using recount, please post at with the “recount” tag.


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