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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.


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


  • 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_
  • Collection: Bioconductor


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.
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.
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.
PMID: 15461798
PMCID: PMC545600

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