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

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Documentation for package ‘circRNAprofiler’ version 1.22.0

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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
mergedBSJunctions mergedBSJunctions
mergeMotifs Group motifs shared by multiple RBPs
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