bcbioRNASeq: R package for bcbio RNA-seq analysis

  • Steinbaugh M
  • Pantano L
  • Kirchner R
  • et al.
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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.

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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

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