qusage
qusage: Quantitative Set Analysis for Gene Expression
Bioconductor version: Release (3.20)
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("qusage")
):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
Reference Manual |
Details
biocViews | GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software |
Version | 2.40.0 |
In Bioconductor since | BioC 2.13 (R-3.0) (11 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 |
See More
Suggests | |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | mExplorer |
Suggests Me | SigCheck |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | qusage_2.40.0.tar.gz |
Windows Binary (x86_64) | qusage_2.40.0.zip |
macOS Binary (x86_64) | qusage_2.40.0.tgz |
macOS Binary (arm64) | qusage_2.39.0.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 |