calculateCoverageProfile
                        calculateCoverageProfile
calculateCoverageProfileFromTxdb
                        calculateCoverageProfileFromTxdb
calculateCoverageProfileList
                        calculateCoverageProfileList
calculateCoverageProfileListFromTxdb
                        calculateCoverageProfileListFromTxdb
createControlRegions    createControlRegions
createDB                createDB
createOrthologousGeneSetList
                        createOrthologousMsigdbDataset
deleteSampleDataFromDB
                        deleteSampleDataFromDB
discoverFeatureSpecificMotifs
                        discoverFeatureSpecificMotifs
extractSequences        extractSequences
geneSets                Random test gene sets
getFeatureBoundaryCoverage
                        getFeatureBoundaryCoverage
getFeatureBoundaryCoverageBin
                        getFeatureBoundaryCoverageBin
getFeatureBoundaryCoverageMulti
                        getFeatureBoundaryCoverageMulti
getIntervalOverlapMatrix
                        getIntervalOverlapMatrix
getMotifSummaryTable    getMotifSummaryTable
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 This function is
                        used to print a MSIGDB dataset into a file.
                        Mostly useful when human data is mapped to
                        another species, and that mapping is required
                        to run the report.
queryGff                queryGff
queryRegions            Sample BED file imported as a GRanges object
retrieveOrthologs       retrieveOrthologs
runGSEA                 runGSEA
runMotifRG              runMotifRG
runReport               Generate a RCAS Report for a list of
                        transcriptome-level segments
runReportMetaAnalysis   runReportMetaAnalysis
runTopGO                runTopGO
summarizeDatabaseContent
                        summarizeDatabaseContent
summarizeQueryRegions   summarizeQueryRegions
summarizeQueryRegionsMulti
                        summarizeQueryRegionsMulti
