mvGST
This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see mvGST.
Multivariate and directional gene set testing
Bioconductor version: 3.6
mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.
Author: John R. Stevens and Dennis S. Mecham
Maintainer: John R. Stevens <john.r.stevens at usu.edu>
citation("mvGST")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mvGST")
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("mvGST")| mvGST Tutorial Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GO, GeneSetEnrichment, GraphAndNetwork, Microarray, OneChannel, Pathways, RNASeq, Software |
| Version | 1.12.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.10.0), GO.db, Rgraphviz |
| Imports | gProfileR, stringr, topGO, GOstats, annotate, AnnotationDbi, graph |
| System Requirements | |
| URL |
See More
| Suggests | hgu133plus2.db, org.Hs.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mvGST_1.12.2.tar.gz |
| Windows Binary | mvGST_1.12.2.zip |
| Mac OS X 10.11 (El Capitan) | mvGST_1.12.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mvGST |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mvGST |
| Package Short Url | https://bioconductor.org/packages/mvGST/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |