BcbioRNAseq: R package for bcbio rna-seq analysis
MJ Steinbaugh, L Pantano, RD Kirchner, V Barrera, BA Chapman, ME Piper, M Mistry, RS Khetani, KD Rutherford, O Hofmann, JN Hutchinson, SH Sui
F1000Research | Published : 2018
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, objects and wrapper functions to post-process bcbio RNA sequencing output data. bcbioRNASeq helps automate the generation of high-level RNA-seq reports, facilitating the quality control analyses, identification of differentially expressed genes and functional enrichment analyses.