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qusage

This is the development version of qusage; for the stable release version, see qusage.

qusage: Quantitative Set Analysis for Gene Expression


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Running qusage PDF R Script
Reference Manual PDF

Details

biocViews GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software
Version 2.37.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL (>= 2)
Depends R (>= 2.10), limma(>= 3.14), methods
Imports utils, Biobase, nlme, emmeans, fftw
System Requirements
URL http://clip.med.yale.edu/qusage
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Package Archives

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

Source Package qusage_2.37.0.tar.gz
Windows Binary qusage_2.37.0.zip
macOS Binary (x86_64) qusage_2.37.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/qusage
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qusage
Bioc Package Browser https://code.bioconductor.org/browse/qusage/
Package Short Url https://bioconductor.org/packages/qusage/
Package Downloads Report Download Stats