recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe

Research output: Contribution to journalArticlepeer-review

Abstract

The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recount Bioconductor package. This workflow explains in detail how to use the recount package and how to integrate it with other Bioconductor packages for several analyses that can be carried out with the recount2 resource. In particular, we describe how the coverage count matrices were computed in recount2 as well as different ways of obtaining public metadata, which can facilitate downstream analyses. Step-by-step directions show how to do a gene-level differential expression analysis, visualize base-level genome coverage data, and perform an analyses at multiple feature levels. This workflow thus provides further information to understand the data in recount2 and a compendium of R code to use the data.

Original languageEnglish (US)
Article number1558
JournalF1000Research
Volume6
DOIs
StatePublished - 2017

Keywords

  • Bioconductor
  • Bioinformatics
  • Differential expression
  • GTEx
  • Genomics
  • Human
  • RNA-seq
  • SRA
  • TCGA
  • Visualization

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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