malhamdoosh/EGSEA
Ensemble of Gene Set Enrichment Analyses

Package index
Search the malhamdoosh/EGSEA package
Vignettes
Functions
165
Source code
23
Man pages
7
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malhamdoosh/EGSEA: Ensemble of Gene Set Enrichment Analyses
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API

API for malhamdoosh/EGSEA
Ensemble of Gene Set Enrichment Analyses

Global 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
arraydata Man page
buildCustomIdx Man page Source code
buildCustomIdx,egsea-index Man page
buildGMTIdx Man page Source code
buildGMTIdx,egsea-index Man page
buildGeneSetDBIdx Man page Source code
buildGeneSetDBIdx,egsea-index Man page
buildIdx Man page Source code
buildIdx,egsea-index Man page
buildKEGGIdx Man page Source code
buildKEGGIdx,egsea-index Man page
buildMSigDBIdx Man page Source code
buildMSigDBIdx,egsea-index Man page
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,egsea-main Man page
egsea.base Man page Source code
egsea.base,egsea-aux Man page
egsea.cnt Man page Source code
egsea.cnt,egsea-main Man page
egsea.combine Man page Source code
egsea.combine,egsea-aux Man page
egsea.logo Man page Source code
egsea.logo,egsea-aux Man page
egsea.ma Man page Source code
egsea.main Source code
egsea.ora Man page Source code
egsea.ora,egsea-main Man page
egsea.selectTopGeneSets Source code
egsea.sort Man page Source code
egsea.sort,egsea-aux Man page
extractAdjPvaluesRanks Source code
extractPvaluesRanks Source code
fisher.method Source code
fisher.sum 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
generateMainReport Source code
generateMainReport.sub 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
limmaTopTable Man page
limmaTopTable,EGSEAResults-method Man page
loadArrayData Source code
loadGeneSetDBCategoryLabels Source code
loadKeggData Source code
loadTopGOdata Source code
makeContrastPairs Source code
mapProbesIntoEntrezIDs 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
runStandardLimmaDEA 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
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
malhamdoosh/EGSEA documentation built on Jan. 28, 2024, 1:17 p.m.

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