mvGST: Multivariate and directional gene set testing

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mvGST")
AuthorJohn R. Stevens and Dennis S. Mecham
Bioconductor views DifferentialExpression GO GeneSetEnrichment GraphAndNetwork Microarray OneChannel Pathways RNASeq
Date of publicationNone
MaintainerJohn R. Stevens <john.r.stevens@usu.edu>
LicenseGPL-3
Version1.10.0

View on Bioconductor

Functions

changeTO10 Man page
combinePvalues Man page
convertPvalues Man page
cut Man page
distributeWeight Man page
fillInList Man page
finalResults Man page
geneNameConvertRows Man page
generateGeneSets Man page
getAncestorsAndOffspring Man page
getCurrentChildren Man page
go2GeneSet Man page
go2Profile Man page
graphCell Man page
hartung Man page
interactiveGraph Man page
makeCoherent Man page
method2 Man page
method3 Man page
method4 Man page
mvGST Man page
mvGSTObject Man page
mvGST-package Man page
mvGSTsamples Man page
mvSort Man page
obatoclax.mvGST Man page
obatoclax.pvals Man page
oneSideBYAdjust Man page
p.adjust.SFL Man page
parathyroid.mvGST Man page
parathyroid.pvals Man page
pickOut Man page
print.mvGST Man page
print.summary.mvGST Man page
profileCombine Man page
profiles Man page
profileTable Man page
separate Man page
summary.mvGST Man page
tableColumns Man page
turnListAround Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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