EGSEA: Ensemble of Gene Set Enrichment Analyses
Version 1.4.0

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

AuthorMonther Alhamdoosh, Milica Ng and Matthew Ritchie
Bioconductor views DifferentialExpression GO GeneExpression GeneSetEnrichment Genetics GraphAndNetwork KEGG Metabolomics Microarray MultipleComparison OneChannel Pathways Proteomics RNASeq Sequencing Software SystemsBiology TwoChannel
Date of publicationNone
MaintainerMonther Alhamdoosh <m.hamdoosh@gmail.com>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EGSEA")

Getting started

Package overview
README.md

Popular man pages

buildKEGGIdx: Gene Set Collection Index from the KEGG Database
egsea: Ensemble of Gene Set Enrichment Analyses Function
egsea.base: EGSEA Base GSE Methods
egsea.cnt: Ensemble of Gene Set Enrichment Analyses Function
egsea.ora: Over-representation Analysis with EGSEA Reporting...
EGSEA-package: Ensemble of Gene Enrichment Analysis (EGSEA)
EGSEAResults-methods: The EGSEAResults class
See all...

All man pages Function index File listing

Man pages

buildCustomIdx: Custom Gene Set Collection Index
buildGeneSetDBIdx: Gene Set Collection Indexes from the GeneSetDB Database
buildIdx: Generate Gene Set Collection Indexes from the MSigDB and KEGG...
buildKEGGIdx: Gene Set Collection Index from the KEGG Database
buildMSigDBIdx: Gene Set Collection Indexes from the MSigDB Database
egsea: Ensemble of Gene Set Enrichment Analyses Function
egsea.base: EGSEA Base GSE Methods
egsea.cnt: Ensemble of Gene Set Enrichment Analyses Function
egsea.combine: EGSEA P-value Combining Options
egsea.ora: Over-representation Analysis with EGSEA Reporting...
EGSEA-package: Ensemble of Gene Enrichment Analysis (EGSEA)
EGSEAResults-methods: The EGSEAResults class
egsea.sort: EGSEA Result Sorting Options
GSCollectionIndex-methods: The GSCollectionIndex class

Functions

$,EGSEAResults-method Man page
$,GSCollectionIndex-method Man page
EGSEA Man page
EGSEA-package Man page
EGSEAResults Man page
EGSEAResults-class Man page
GSCollectionIndex Man page
GSCollectionIndex-class Man page
anyOccur Source code
buildCustomIdx Man page Source code
buildGeneSetDBIdx Man page Source code
buildIdx Man page Source code
buildKEGGIdx Man page Source code
buildMSigDBIdx Man page Source code
calculateSetScores Source code
calculateSetScores.parallel Source code
combineBaseGSEAs Source code
combinePvalues Source code
createComparison Source code
createEGSEAReport Source code
createSummaryHeatmap Source code
egsea Man page Source code
egsea.base Man page Source code
egsea.cnt Man page Source code
egsea.combine Man page Source code
egsea.logo Man page Source code
egsea.main Source code
egsea.ora Man page Source code
egsea.selectTopGeneSets Source code
egsea.sort Man page Source code
extractAdjPvaluesRanks Source code
extractPvaluesRanks Source code
fisher.method Source code
fisher.sum Source code
generate.EGSEA.Report Source code
generateAllGOgraphsPage Source code
generateAllGOgraphsPage.comparison Source code
generateAllHeatmapsPage Source code
generateAllPathwaysPage Source code
generateComparisonPathway Source code
generateGOGraphs Source code
generateHeatMap Source code
generateMDSMethodsPlot Source code
generatePathway Source code
generatePlotData Source code
generatePlotData.comparison Source code
generateReport Man page
generateReport,EGSEAResults-method Man page
generateSumPlots Source code
generateSumPlots.comparison Source code
generateSummaryHeatmaps Source code
generateSummaryPage Source code
generateSummaryPage.comparison Source code
generateSummaryPlots Source code
generateSummaryPlots.comparison Source code
get.toptables Source code
getBaseInfo Source code
getNumberofSamples Source code
getSetByID Man page
getSetByID,GSCollectionIndex-method Man page
getSetByName Man page
getSetByName,GSCollectionIndex-method Man page
getSetScores Man page
getSetScores,EGSEAResults-method Man page
getlimmaResults Man page
getlimmaResults,EGSEAResults-method Man page
getlogFCFromLMFit Source code
limmaTopTable Man page
limmaTopTable,EGSEAResults-method Man page
loadGeneSetDBCategoryLabels Source code
loadKeggData Source code
loadTopGOdata Source code
normalizeSpecies Source code
optimizeNumThreads Source code
plotBars Man page
plotBars,EGSEAResults-method Man page
plotGOGraph Man page
plotGOGraph,EGSEAResults-method Man page
plotGOGraphs Source code
plotGOGraphs.comparison Source code
plotHeatMapsLogFC Source code
plotHeatMapsLogFC.comparison Source code
plotHeatmap Man page
plotHeatmap,EGSEAResults-method Man page
plotMethods Man page
plotMethods,EGSEAResults-method Man page
plotPathway Man page
plotPathway,EGSEAResults-method Man page
plotPathways Source code
plotPathways.comparison Source code
plotSummary Man page
plotSummary,EGSEAResults-method Man page
plotSummaryHeatmap Man page
plotSummaryHeatmap,EGSEAResults-method Man page
prepareTwoGroupsData Source code
runbaseGSEA Source code
runbaseGSEAParallelWorker Source code
runcamera Source code
runcamera.contrast Source code
runegsea Source code
runfry Source code
runfry.contrast Source code
rungage Source code
rungage.contrast Source code
runglobaltest Source code
runglobaltest.contrast Source code
rungsva Source code
rungsva.subcollection Source code
runora Source code
runora.collection Source code
runpadog Source code
runpadog.contrast Source code
runroast Source code
runroast.contrast Source code
runsafe Source code
runsafe.contrast Source code
show,EGSEAResults-method Man page
show,GSCollectionIndex-method Man page
showSetByID Man page
showSetByID,EGSEAResults-method Man page
showSetByName Man page
showSetByName,EGSEAResults-method Man page
summary,EGSEAResults-method Man page
summary,GSCollectionIndex-method Man page
topDiffGenes Source code
topSets Man page
topSets,EGSEAResults-method Man page
voteRank Source code
write.base.results Source code
write.base.stats Source code
writeEGSEAResultsToHTML Source code
writeResultsToHTML Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/EGSEAclass.R
R/GSCollectionIndexclass.R
R/egsea.R
R/egseaReport.R
R/egseaUtils.R
R/fisher.method.R
R/gsacamera.R
R/gsafry.R
R/gsagage.R
R/gsaglobaltest.R
R/gsagsva.R
R/gsaora.R
R/gsapadog.R
R/gsaplots.R
R/gsaroast.R
R/gsasafe.R
R/htmlUtils.R
R/idxAnno.R
R/wrapperUtils.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/EGSEA.R
inst/doc/EGSEA.Rnw
inst/doc/EGSEA.pdf
inst/logo
inst/logo/EGSEA_logo.png
man
man/EGSEA-package.Rd
man/EGSEAResults-methods.Rd
man/GSCollectionIndex-methods.Rd
man/buildCustomIdx.Rd
man/buildGeneSetDBIdx.Rd
man/buildIdx.Rd
man/buildKEGGIdx.Rd
man/buildMSigDBIdx.Rd
man/egsea.Rd
man/egsea.base.Rd
man/egsea.cnt.Rd
man/egsea.combine.Rd
man/egsea.ora.Rd
man/egsea.sort.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_EGSEA.R
vignettes
vignettes/EGSEA.Rnw
vignettes/egsea_classes-crop.pdf
vignettes/egsea_report-crop.pdf
vignettes/egsea_results-crop.pdf
vignettes/references.bib
EGSEA documentation built on May 20, 2017, 9:19 p.m.

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