RT Journal Article SR Electronic T1 recount: A large-scale resource of analysis-ready RNA-seq expression data JF bioRxiv FD Cold Spring Harbor Laboratory SP 068478 DO 10.1101/068478 A1 Leonardo Collado-Torres A1 Abhinav Nellore A1 Kai Kammers A1 Shannon E. Ellis A1 Margaret A. Taub A1 Kasper D. Hansen A1 Andrew E. Jaffe A1 Ben Langmead A1 Jeffrey T. Leek YR 2016 UL http://biorxiv.org/content/early/2016/08/08/068478.abstract AB 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 Bio-conductor 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/.