mvGST

Package: mvGST
Type: Package
Title: Multivariate and directional gene set testing
Version: 1.6.0
Date: 2014-10-02
Author: John R. Stevens and Dennis S. Mecham
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Description: 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.
Depends: R (>= 2.10.0), GO.db, Rgraphviz
Imports: gProfileR, stringr, topGO, GOstats, annotate, AnnotationDbi,
graph
Suggests: hgu133plus2.db, org.Hs.eg.db
License: GPL-3
biocViews: Microarray, OneChannel, RNASeq, DifferentialExpression, GO,
Pathways, GeneSetEnrichment, GraphAndNetwork
NeedsCompilation: no
Packaged: 2016-05-05 04:50:02 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'mvGST' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mvGST'
    finding HTML links ... done
    go2Profile                              html  
    graphCell                               html  
    mvGST-package                           html  
    mvGST.other                             html  
    mvGSTsamples                            html  
    p.adjust.SFL                            html  
    pickOut                                 html  
    profileTable                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mvGST)
Making 'packages.html' ... done