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goseq

goseq

goseq is a tool for functional profiling by analysis of gene ontology (GO) of RNA_seq data. The goseq algorithm can also estimate the effect of bias.

Topic

RNA-Seq; Gene expression

Details

  • Operation: Gene functional annotation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU Lesser General Public License v>=2
  • Cost: Free
  • Version name: 1.38.0
  • Maturity: Mature
  • Credit: -
  • Contact: Nadia Davidson nadia.davidson _at_ mcri.edu.au | Matthew Young my4 at sanger.ac.u
  • Collection: Bioconductor

Publications

Young MD, Wakefield MJ, Smyth GK, Oshlack A "Gene ontology analysis for RNA-seq: accounting for selection bias." Genome Biol. 2010;11(2):R14. https://doi.org/10.1186/gb-2010-11-2-r14
PMID: 20132535
PMCID: PMC2872874


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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