calculateCoverageProfile
                        calculateCoverageProfile
calculateCoverageProfileFromTxdb
                        calculateCoverageProfileFromTxdb
calculateCoverageProfileList
                        calculateCoverageProfileList
calculateCoverageProfileListFromTxdb
                        calculateCoverageProfileListFromTxdb
checkSeqDb              checkSeqDb
createControlRegions    createControlRegions
createDB                createDB
createOrthologousGeneSetList
                        createOrthologousMsigdbDataset This function is
                        deprecated. For functional enrichment analysis,
                        use findEnrichedFunctions.
deleteSampleDataFromDB
                        deleteSampleDataFromDB
discoverFeatureSpecificMotifs
                        discoverFeatureSpecificMotifs
extractSequences        extractSequences
findDifferentialMotifs
                        Find Differential Motifs
findEnrichedFunctions   findEnrichedFunctions
generateKmers           Generate K-mers
getFeatureBoundaryCoverage
                        getFeatureBoundaryCoverage
getFeatureBoundaryCoverageBin
                        getFeatureBoundaryCoverageBin
getFeatureBoundaryCoverageMulti
                        getFeatureBoundaryCoverageMulti
getIntervalOverlapMatrix
                        getIntervalOverlapMatrix
getMotifSummaryTable    getMotifSummaryTable
getPWM                  getPWM
getTargetedGenesTable   getTargetedGenesTable
getTxdbFeatures         getTxdbFeatures
getTxdbFeaturesFromGRanges
                        getTxdbFeaturesFromGRanges
gff                     Sample GFF file imported as a GRanges object
importBed               importBed
importBedFiles          importBedFiles
importGtf               importGtf
parseMsigdb             parseMsigdb
plotFeatureBoundaryCoverage
                        plotFeatureBoundaryCoverage
printMsigdbDataset      Print MSIGDB Dataset to a file
queryGff                queryGff
queryRegions            Sample BED file imported as a GRanges object
retrieveOrthologs       retrieveOrthologs
runGSEA                 runGSEA
runMotifDiscovery       runMotifDiscovery
runMotifRG              run motifRG
runReport               Generate a RCAS Report for a list of
                        transcriptome-level segments
runReportMetaAnalysis   runReportMetaAnalysis
runTopGO                runTopGO
summarizeDatabaseContent
                        summarizeDatabaseContent
summarizeQueryRegions   summarizeQueryRegions
summarizeQueryRegionsMulti
                        summarizeQueryRegionsMulti
