Last data update: 2014.03.03
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SeqGSEA
Package: SeqGSEA
Type: Package
Title: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating
differential expression and splicing
Version: 1.12.0
Date: 2015-08-21
Author: Xi Wang <Xi.Wang@newcastle.edu.au>
Maintainer: Xi Wang <Xi.Wang@mdc-berlin.de>
Description: The package generally provides methods for gene set
enrichment analysis of high-throughput RNA-Seq data by
integrating differential expression and splicing. It uses
negative binomial distribution to model read count data, which
accounts for sequencing biases and biological variation. Based
on permutation tests, statistical significance can also be
achieved regarding each gene's differential expression and
splicing, respectively.
License: GPL (>= 3)
Depends: Biobase, doParallel, DESeq
Imports: methods, biomaRt
Suggests: easyRNASeq, GenomicRanges
biocViews: Sequencing, RNASeq, GeneSetEnrichment, GeneExpression,
DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-05 03:51:13 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SeqGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'SeqGSEA'
finding HTML links ... done
DENBStat4GSEA html
DENBStatPermut4GSEA html
DENBTest html
DEpermutePval html
DEscore html
DSpermute4GSEA html
DSpermutePval html
DSresultExonTable html
DSresultGeneTable html
GSEAresultTable html
GSEnrichAnalyze html
GS_example html
RCS_example html
ReadCountSet-class html
finding level-2 HTML links ... done
SeqGSEA-package html
SeqGeneSet-class html
calES html
calES.perm html
convertEnsembl2Symbol html
convertSymbol2Ensembl html
counts-methods html
estiExonNBstat html
estiGeneNBstat html
exonID html
exonTestability html
geneID html
geneList html
genePermuteScore html
geneScore html
geneSetDescs html
geneSetNames html
geneSetSize html
geneTestability html
genpermuteMat html
getGeneCount html
label html
loadExonCountData html
loadGenesets html
newGeneSets html
newReadCountSet html
normES html
normFactor html
plotES html
plotGeneScore html
plotSig html
plotSigGeneSet html
rankCombine html
runDESeq html
runSeqGSEA html
scoreNormalization html
signifES html
size html
subsetByGenes html
topDEGenes html
topDSExons html
topDSGenes html
topGeneSets html
writeScores html
writeSigGeneSet html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqGSEA)
Making 'packages.html' ... done
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