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

qusage

qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: 2.13

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>

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	Bioinformatics, Enrichment, GeneSetEnrichment, Microarrays, RNAseq, Software
Version	1.2.0
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

Follow Installation instructions to use this package in your R session.

Package Source	qusage_1.2.0.tar.gz
Windows Binary	qusage_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	qusage_1.2.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats