Man pages for circRNAprofiler
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

ahChainFilesahChainFile
ahRepeatMaskerahRepeatMasker
annotateBSJsAnnotate circRNA features.
annotateRepeatsAnnotate repetitive elements
annotateSNPsGWASAnnotate GWAS SNPs
attractSpeciesattractSpecies
backSplicedJunctionsbackSplicedJunctions
checkProjectFolderCheck project folder
filterCircFilter circRNAs
formatGTFFormat annotation file
getBackSplicedJunctionsImport detected circRNAs
getCircSeqsRetrieve circRNA sequences
getDeseqResDifferential circRNA expression analysis adapted from DESeq2
getDetectionToolsCreate data frame with circRNA detection codes
getEdgerResDifferential circRNA expression analysis adapted from EdgeR
getMiRsitesScreen target sequences for miR binding sites
getMotifsScreen target sequences for recurrent motifs
getRandomBSJunctionsRetrieve random back-spliced junctions
getRegexPatternConvert IUPAC sequence to an regular expression
getSeqsAcrossBSJsRetrieve back-spliced junction sequences
getSeqsFromGRsRetrieve sequences flanking back-spliced junctions
gtfgtf
gwasTraitsgwasTraits
importCircExplorer2Import circRNAs detected by CircExplorer2
importCircMarkerImport circRNAs detected by CircMarker
importKnifeImport circRNAs detected by KINFE
importMapSpliceImport circRNAs detected by MapSplice2
importNCLscanImport circRNAs detected by NCLscan
importOtherImport circRNAs detected by an annotation-based circRNA...
importUroborusImport circRNAs detected by UROBORUS
initCircRNAprofilerInitialize the project folder
iupaciupac
liftBSJcoordsLiftOver back-spliced junction coordinates
mergeBSJunctionsGroup circRNAs identified by multiple prediction tools
mergedBSJunctionsmergedBSJunctions
mergeMotifsGroup motifs shared by multiple RBPs
miRspeciesCodesmiRspeciesCodes
plotExBetweenBSEsPlot exons between back-spliced junctions
plotExPositionPlot back-spliced exon positions
plotHostGenesPlot circRNA host genes
plotLenBSEsPlot length back-spliced exons
plotLenIntronsPlot length introns flanking back-spliced junctions
plotMiRPlot miRNA analysis results
plotMotifsPlot motifs analysis results
plotTotExonsPlot exons in the circRNA host transcript
rearrangeMiRresRearrange miR results
volcanoPlotPlot differential circRNA expression results
circRNAprofiler documentation built on Oct. 31, 2019, 3:23 a.m.