qusage

DOI: 10.18129/B9.bioc.qusage    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see qusage.

qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: 3.14

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. The QuSAGE package also includes a mixed effects model implementation, as described in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as described in (Meng H, et al. PLoS Comput Biol. 2019). 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, Hailong Meng, Jacob Turner, Derek Blankenship, and Steven Kleinstein

Maintainer: Christopher Bolen <cbolen1 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qusage")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Microarray, RNASeq, Software
Version	2.28.0
In Bioconductor since	BioC 2.13 (R-3.0) (8.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), limma(>= 3.14), methods
Imports	utils, Biobase, nlme, emmeans, fftw
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://clip.med.yale.edu/qusage
Depends On Me
Imports Me	mExplorer
Suggests Me	NanoTube, SigCheck
Links To Me
Build Report

Package Archives

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

Source Package	qusage_2.28.0.tar.gz
Windows Binary	qusage_2.28.0.zip
macOS 10.13 (High Sierra)	qusage_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/qusage
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/qusage
Package Short Url	https://bioconductor.org/packages/qusage/
Package Downloads Report	Download Stats