To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("qusage")

In most cases, you don't need to download the package archive at all.

qusage

qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: Release (2.14)

This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

Author: Christopher Bolen and Gur Yaari, with contributions from Juilee Thakar and Steven Kleinstein

Maintainer: Christopher Bolen <cbolen1 at gmail.com>

Citation (from within R, enter citation("qusage")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("qusage")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("qusage")

 

PDF R Script Running qusage
PDF   Reference Manual

Details

biocViews GeneSetEnrichment, Microarray, RNASeq, Software
Version 1.4.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL (>= 2)
Depends R (>= 2.10), limma(>= 3.14), methods
Imports utils, Biobase
Suggests
System Requirements
URL http://clip.med.yale.edu/qusage
Depends On Me
Imports Me
Suggests Me

Package Archives

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Package Source qusage_1.4.0.tar.gz
Windows Binary qusage_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) qusage_1.4.0.tgz
Mac OS X 10.9 (Mavericks) qusage_1.4.0.tgz
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