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QuSAGE | A method to quantify gene set differential expression including gene-gene correlations

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A computational framework for quantitative set analysis of gene expression. QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than evaluating the deviation from a null hypothesis with a P-value, it quantifies gene-set activity with a complete probability density function. From this probability density function, P-values and confidence intervals can be extracted and post hoc analysis can be carried out while maintaining statistical traceability. Compared with Gene Set Enrichment Analysis and CAMERA, QuSAGE exhibits better sensitivity and specificity on real data profiling the response to interferon therapy (in chronic Hepatitis C virus patients) and Influenza A virus infection.

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QuSAGE forum

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QuSAGE classification

QuSAGE specifications

Unique identifier:
OMICS_09761
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Name:
Quantitative Set Analysis for Gene Expression
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.8.0
Requirements:
limma, methods

QuSAGE distribution

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QuSAGE support

Documentation

Maintainer

  • Christopher R. Bolen <>

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