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| 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 |
| 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 |