GAGE specifications

Unique identifier:
OMICS_18498
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
2.26.0
Maintained:
Yes
Name:
Generally Applicable Gene-set Enrichment
Interface:
Command line interface
Input data:
A gene set.
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

versioning

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GAGE distribution

download

GAGE support

Documentation

Maintainers

  • Peter Woolf <>
  • Weijun Luo <>
  • Michael Friedman <>
  • Kerby Shedden <>
  • Kurt Hankenson <>

Additional information

https://github.com/Bioconductor-mirror/gage/tree/release-3.5

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Credits

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Publications

Institution(s)

Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Bioinformatics Shared Resource, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Thermogenesis Corporation, Rancho Cordova, CA, USA; Department of Statistics, University of Michigan, Ann Arbor, MI, USA; Department of Animal Biology, University of Pennsylvania, Philadelphia, PA, USA; Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA

Funding source(s)

Supported by NIH grant R01 DE017471; by NIH grant U54-DA-021519 and by NIH grants R01 AR054714 and R01 AR049682.

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1 user review

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Dr Nick

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A fairly easy algorithm and R package to perform custom gene set enrichment analyses with normalized expression datasets. My only qualm is the lack of information and examples to assist in the guidance of variable universe sizes among different datasets. A Fisher's test is very explicit in the effects of a changing universe size, but have had to empirically test, through numerous iterations, the equivalency of one sets enrichment results to another using the same reference set for comparison. Regardless, the ease of implementation compared with other popular packages, such as GSEA, make it possible to iteratively test such parameter changes in short order.

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