bcbioRNASeq is a tool for the analysis deferentially expressed genes in RNA-seq data. The package includes a workflow for pre-processing, identification of deferentially expressed genes, annotation, and reporting .
RNA-seq; Transcriptomics
Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui "bcbioRNASeq: R package for bcbio RNA-seq analysis" F1000Research https://doi.org/10.12688/f1000research.12093.2
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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