# RNA Centric Annotation System

## Documentation for package ‘RCAS’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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