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SeqGSEA

SeqGSEA

SeqGSEA is an R tool for gene enrichment analysis (GSEA) of RNA-seq data. The SeqGSEA algorithm uses a negative binomial distribution model for count data, computes and scores differential splicing and expression, estimates for biological variability, and gene set enrichment analysis (GSEA).

Topic

RNA-Seq; Gene expression

Details

  • Operation: Gene-set enrichment analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=3
  • Cost: Free
  • Version name: 1.26.0
  • Credit: The Schizophrenia Research Institute; NSW Health and the Henderson Foundation, National Health and Medical Research Council, M.C. Ainsworth Research Fellowship in Epigenetics.
  • Contact: Xi Wang Xi.Wang _at_ mdc-berlin.de
  • Collection: Bioconductor

Publications

Wang X, Cairns MJ "SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing." Bioinformatics. 2014 Jun 15;30(12):1777-9. Epub 2014 Feb 17. https://doi.org/10.1093/bioinformatics/btu090
PMID: 24535097


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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