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

Abstract

The recount2 project re-processed RNA sequencing (RNA-seq) data on over 70,000 human RNA-seq samples spanning a variety of tissues, cell types and disease conditions. Researchers can easily access these data via the recount Bioconductor package, and can quickly import gene, exon, exon-exon junction, transcript and base-pair coverage data for uniformly processed data from the SRA, GTEx and TCGA projects in R for analysis. This talk will cover different use cases of the recount package, including downloading and normalizing data, processing and cleaning relevant phenotype data, performing differential expression (DE) analyses, and creating reports for exploring the results using other Bioconductor packages.

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