spliceR is a tool to classify alternative splicing and assess the coding potential of RNA-seq data. The spliceR algorithm can detect exon skipping, intron retention, alternative first or last exon usage, donor and acceptor sites, and mutually exclusive exon events. spliceR produces genomic coordinates for all differentially spliced sequences and predicts the coding potential and possible nonsense-mediated decay for each of the transcripts.
RNA-Seq; RNA splicing
Vitting-Seerup K, Porse BT, Sandelin A, Waage J "spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data." BMC Bioinformatics 2014 https://doi.org/10.1186/1471-2105-15-81
PMID: 24655717
PMCID: PMC3998036
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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