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

## Documentation for package ‘circRNAprofiler’ version 1.0.0

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

## Help Pages

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
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