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GAGE

GAGE

GAGE (Generally Applicable Gene-set Enrichment) is a tool for gene set enrichment (GSEA) and pathway analysis of RNA-seq and microarray data. The GAGE package contains functions for GSEA, processing of results, reporting, batch analyses, and comparison between studies.

Topic

RNA-Seq; Gene expression; Molecular interactions, pathways and networks; Genetics

Details

  • Operation: Pathway or network analysis; Gene-set enrichment analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v>=2
  • Cost: Free
  • Version name: 2.36.0
  • Maturity: Mature
  • Credit: The National Institutes of Health (NIH).
  • Contact: Weijun Luo luo_weijun _at_ yahoo.com
  • Collection: Bioconductor

Publications

Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ "GAGE: generally applicable gene set enrichment for pathway analysis." BMC Bioinformatics. 2009 May 27;10:161. https://doi.org/10.1186/1471-2105-10-161
PMID: 19473525
PMCID: PMC2696452


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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