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

By Leonardo Collado-Torres, Abhinav Nellore, Kai Kammers, Shannon E. Ellis, Margaret A Taub, Kasper D. Hansen, Andrew E. Jaffe, Ben Langmead, Jeffrey T Leek

Posted 08 Aug 2016
bioRxiv DOI: 10.1101/068478

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. We also provide data summarization types for quantifying novel transcribed sequence including base-resolution coverage and potentially unannotated splice junctions. We 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. The resource is available at https://jhubiostatistics.shinyapps.io/recount/.

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