bcbioRNASeq R package for bcbio RNA-seq analysis

M Steinbaugh,L Pantano,R Kirchner,V Barrera,B Chapman,M Piper,M Mistry,R Khetani,K Rutherford,O Hofmann,J Hutchinson,S Ho

Abstract

RNA-seq analysis involves multiple steps from processing raw sequencing data to identifying, organizing, annotating, and reporting differentially expressed genes. bcbio is an open source, community-maintained framework providing automated and scalable RNA-seq methods for identifying gene abundance counts. We have developed bcbioRNASeq, a Bioconductor package that provides ready-to-render templates and wrapper functions to post-process bcbio output data. bcbioRNASeq automates the generation of high-level RNA-seq reports, including identification of differentially expressed genes, functional enrichment analysis and quality control analysis.