SigFuge is a tool to identify genomic loci that display differential expression patterns among several RNA-seq datasets. The SigFuge algorithm uses hypothesis testing to asses clustered genes that manifest alternative splicing or differences of isoform expression.
RNA-Seq; Gene expression; Data visualisation; RNA
Kimes PK, Cabanski CR, Wilkerson MD, Zhao N, Johnson AR, Perou CM, Makowski L, Maher CA, Liu Y, Marron JS, Hayes DN "SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples." Nucleic Acids Res. 2014; 42(14):e113 https://doi.org/10.1093/nar/gku521
PMID: 25030904
PMCID: PMC4132703
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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