This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

qusage

qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: Release (3.17)

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 "4.3") 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")
Running qusage PDF R Script
Reference Manual PDF

Details

biocViews GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software
Version 2.34.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License GPL (>= 2)
Depends R (>= 2.10), limma(>= 3.14), methods
Imports utils, Biobase, nlme, emmeans, fftw
Linking To
Suggests
System Requirements
Enhances
URL http://clip.med.yale.edu/qusage
See More
Depends On Me
Imports Me mExplorer
Suggests Me SigCheck
Links To Me
Build Report  

Package Archives

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

Source Package qusage_2.34.0.tar.gz
Windows Binary qusage_2.34.0.zip
macOS Binary (x86_64) qusage_2.34.0.tgz
macOS Binary (arm64) qusage_2.34.0.tgz
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