DaMiRseq is an R tool to select features, classification, and bias removal of RNA-seq data. The input consists of raw counts. DaMiRseq has visualization functions for heatmaps, RLE, MDS, or correlation plots.
Data mining; RNA-seq; Statistics and probability; Sequencing; RNA-seq
Chiesa M, Colombo GI, Piacentini L "DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification." Bioinformatics. 2018 Apr 15;34(8):1416-1418. https://doi.org/10.1093/bioinformatics/btx795
PMID: 29236969
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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