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| calculateCoverageProfile | calculateCoverageProfile |
| calculateCoverageProfileFromTxdb | calculateCoverageProfileFromTxdb |
| calculateCoverageProfileList | calculateCoverageProfileList |
| calculateCoverageProfileListFromTxdb | calculateCoverageProfileListFromTxdb |
| createControlRegions | createControlRegions |
| createOrthologousGeneSetList | createOrthologousMsigdbDataset |
| extractSequences | extractSequences |
| geneSets | Random test gene sets |
| getFeatureBoundaryCoverage | getFeatureBoundaryCoverage |
| getFeatureBoundaryCoverageBin | getFeatureBoundaryCoverageBin |
| getMotifSummaryTable | getMotifSummaryTable |
| getTargetedGenesTable | getTargetedGenesTable |
| getTxdbFeatures | getTxdbFeatures |
| getTxdbFeaturesFromGRanges | getTxdbFeaturesFromGRanges |
| gff | Sample GFF file imported as a GRanges object |
| importBed | importBed |
| 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 |
| runTopGO | runTopGO |
| summarizeQueryRegions | summarizeQueryRegions |