An R tool for analysis of splicing pathways. The PathwaySplice algorithm adjusts the number of exon junctions, visualizes a selection bias, supports Gene Ontology terms, user-defined gene sets, distinguishes primary genes in a pathway, and arranges pathways into an enrichment map.
RNA splicing; RNA-seq; Molecular interactions, pathways and networks
Yan A, Ban Y, Gao Z, Chen X, Wang L "PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data." Bioinformatics. 2018 Sep 15;34(18):3220-3222. https://doi.org/10.1093/bioinformatics/bty317
PMID: 29688305
PMCID: PMC6137985
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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