QuSAGE specifications


Unique identifier OMICS_09761
Alternative name Quantitative Set Analysis for Gene Expression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.14.0
Stability Stable
methods, Biobase, utils, R(>=2.10), nlme, limma(>=3.14), lsmeans
Maintained Yes


No version available



  • person_outline Christopher R. Bolen

Publication for Quantitative Set Analysis for Gene Expression

QuSAGE citations


Robust multi group gene set analysis with few replicates

BMC Bioinformatics
PMCID: 5148902
PMID: 27938331
DOI: 10.1186/s12859-016-1403-0

[…] ese variables. With regard to the performance of other methods, we speculate that 1) CAMERA appears to favor larger gene sets as it failed slightly in primary data and significantly in mouse data, 2) QuSAGE seems to prefer stronger expression signal as it performed well with primary human cell and mouse data, and 3) Allez performed well on the mouse data and therefore probably favors smaller gene […]


The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles

PMCID: 4678663
PMID: 26667497
DOI: 10.1186/s40168-015-0133-2

[…] D. After filtering, the lmFit and eBayes functions were used to perform moderated paired t testing for each gene across visits 1 and 2.At this level, gene set enrichment of ISG was performed with the QuSAGE package in R [], comparing our processed gene lists against those from a prior study of A549 cell lines subjected to α or γ interferon [].Genes of interest from either group were then selected […]

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