RNA Centric Annotation System


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Documentation for package ‘RCAS’ version 1.20.0

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