Rsubread is an R tool for RNA-/DNA-seq data mapping, read counting, single-nucleotide polymorphism (SNP), structural variant, and gene fusion detection. The tool is also available in C language, see Subread.
Sequencing; Mapping; Whole genome sequencing; RNA-seq
Liao Y, Smyth GK, Shi W "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads." Nucleic Acids Res. 2019 May 7;47(8):e47. https://doi.org/10.1093/nar/gkz114
PMID: 30783653
PMCID: PMC6486549
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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