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
No versioning.
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
forum
No open topic.
Credits
Publications
-
(Luo et al., 2009)
GAGE: generally applicable gene set enrichment for pathway analysis.
BMC Bioinformatics.
PMID: 19473525 DOI: 10.1186/1471-2105-10-161
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.
User review
1 user review
1 user review
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.
