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.
Steinbaugh, M. J., Pantano, L., Kirchner, R. D., Barrera, V., Chapman, B. A., Piper, M. E., … Ho Sui, S. (2017). bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research, 6, 1976. https://doi.org/10.12688/f1000research.12093.1