GSVA specifications

Unique identifier:
OMICS_06741
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Name:
Gene Set Variation Analysis
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.8.0
Requirements:
methods, GSEABase

versioning

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No versioning.

GSVA support

Documentation

Maintainer

  • Justin Guinney <>

forum

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Credits

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Publications

Institution(s)

Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain; Sage Bionetworks, Seattle, WA, USA

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Dr Nick

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If you take the time to dissect and understand the mathematics behind the tool, as well as tweak your R code to format custom reference lists beyond KEGG and GO, it turns out to be a fantastic tool for assessing reference enrichments within your query set on a sample by sample basis. However, be warned that very low sample numbers are problematic, and if you intend to compare conditions, I personally recommend doing so in binary fashion as the scoring is dependent on the universe of your input.

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