ahChainFiles            ahChainFile
ahRepeatMasker          ahRepeatMasker
annotateBSJs            Annotate circRNA features.
annotateRepeats         Annotate repetitive elements
annotateSNPsGWAS        Annotate GWAS SNPs
attractSpecies          attractSpecies
backSplicedJunctions    backSplicedJunctions
checkProjectFolder      Check project folder
filterCirc              Filter circRNAs
formatGTF               Format annotation file
getBackSplicedJunctions
                        Import detected circRNAs
getCircSeqs             Retrieve circRNA sequences
getDeseqRes             Differential circRNA expression analysis
                        adapted from DESeq2
getDetectionTools       Create data frame with circRNA detection codes
getEdgerRes             Differential circRNA expression analysis
                        adapted from EdgeR
getMiRsites             Screen target sequences for miR binding sites
getMotifs               Screen target sequences for recurrent motifs
getRandomBSJunctions    Retrieve random back-spliced junctions
getRegexPattern         Convert IUPAC sequence to an regular expression
getSeqsAcrossBSJs       Retrieve back-spliced junction sequences
getSeqsFromGRs          Retrieve sequences flanking back-spliced
                        junctions
gtf                     gtf
gwasTraits              gwasTraits
initCircRNAprofiler     Initialize the project folder
iupac                   iupac
liftBSJcoords           LiftOver back-spliced junction coordinates
memeDB                  memeDB
mergeBSJunctions        Group circRNAs identified by multiple
                        prediction tools
mergeMotifs             Group motifs shared by multiple RBPs
mergedBSJunctions       mergedBSJunctions
miRspeciesCodes         miRspeciesCodes
plotExBetweenBSEs       Plot exons between back-spliced junctions
plotExPosition          Plot back-spliced exon positions
plotHostGenes           Plot circRNA host genes
plotLenBSEs             Plot length back-spliced exons
plotLenIntrons          Plot length introns flanking back-spliced
                        junctions
plotMiR                 Plot miRNA analysis results
plotMotifs              Plot motifs analysis results
plotTotExons            Plot exons in the circRNA host transcript
rearrangeMiRres         Rearrange miR results
volcanoPlot             Plot differential circRNA expression results
