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

Global functions
.addGeneName Source code
.addMiRid Source code
.checkBSJsDF Source code
.checkExperiment Source code
.checkGTF Source code
.checkMer Source code
.checkMiRs Source code
.checkMiRspeciesCode Source code
.checkMotifs Source code
.checkTraits Source code
.checkTranscripts Source code
.cleanTargets Source code
.compareSequences Source code
.computeMotifs Source code
.createAnnotatedBSJsDF Source code
.createFilteredMotifsDF Source code
.createGRsForLift Source code
.createLiftedBSJCoordsDF Source code
.createMatchesDF Source code
.createMiRsitesList Source code
.createMiRsitesTempDF Source code
.createRandomBSJunctionsDF Source code
.createSNPsGWASlist Source code
.fillMatches Source code
.fillMiRsites Source code
.filterMotifs Source code
.findOverlappingSNPs Source code
.fixCoords Source code
.fixCoordsWithGTF Source code
.getAUcontent Source code
.getAllTranscripts Source code
.getAnnotatedBSJsColNames Source code
.getBSEcoords Source code
.getBSEsFromTranscript Source code
.getBasicColNames Source code
.getCEcolNames Source code
.getCMcolNames Source code
.getCentralMatches Source code
.getChain Source code
.getCompensatoryMatches Source code
.getComplRepeats Source code
.getDeseqResDF Source code
.getEdgerResDF Source code
.getExonSeqs Source code
.getExperimentTemplate Source code
.getFIcoords Source code
.getFlankIntronFirst Source code
.getFlankIntronLast Source code
.getFlankIntrons Source code
.getGRcolNames Source code
.getGRcoordsDF Source code
.getGWAS Source code
.getID Source code
.getIECoords Source code
.getIntronCoords Source code
.getKnColNames Source code
.getLengthBSEfi Source code
.getLengthCirc Source code
.getMScolNames Source code
.getMatches Source code
.getMergedMotifsAll Source code
.getMiRids Source code
.getMiRsFromMiRBase Source code
.getMiRsTemplate Source code
.getMiRseqs Source code
.getMotifsTemplate Source code
.getNScolNames Source code
.getNeededColumn Source code
.getRNAss Source code
.getRepeatsColNames Source code
.getSNPsGWASColNames Source code
.getSeedMatches Source code
.getSeqFromBSgenome Source code
.getT1nucleotide Source code
.getTargetsColNames Source code
.getTargetsDF Source code
.getTopMir Source code
.getTraitsTemplate Source code
.getTranscriptToAnalyze Source code
.getTranscriptsTemplate Source code
.getURcolNames Source code
.getUserDBmotifs Source code
.grCoordsForNegative Source code
.grCoordsForPositive Source code
.matchWithKnowRBPs Source code
.nameMiRsitesListDF Source code
.readExperiment Source code
.readGTF Source code
.readMiRs Source code
.readMotifs Source code
.readPathToFile Source code
.readTraits Source code
.readTranscripts Source code
.recreateBSJseq Source code
.recreateCircSeq Source code
.renameSNPsGWAS Source code
.selectRandomBSEs Source code
.setxyLim Source code
.splitKNprediction Source code
.upperHuman Source code
ahChainFiles Man page
ahRepeatMasker Man page
annotateBSJs Man page Source code
annotateRepeats Man page Source code
annotateSNPsGWAS Man page Source code
attractSpecies Man page
backSplicedJunctions Man page
checkProjectFolder Man page Source code
createMiRsitesInternalDF Source code
filterCirc Man page Source code
formatGTF Man page Source code
getBackSplicedJunctions Man page Source code
getCircSeqs Man page Source code
getDeseqRes Man page Source code
getDetectionTools Man page
getEdgerRes Man page Source code
getMiRsites Man page Source code
getMotifs Man page Source code
getRandomBSJunctions Man page Source code
getRegexPattern Man page Source code
getSeqsAcrossBSJs Man page Source code
getSeqsFromGRs Man page Source code
gtf Man page
gwasTraits Man page
importCircExplorer2 Man page Source code
importCircMarker Man page Source code
importKnife Man page Source code
importMapSplice Man page Source code
importNCLscan Man page Source code
importOther Man page Source code
importUroborus Man page Source code
initCircRNAprofiler Man page Source code
iupac Man page
liftBSJcoords Man page Source code
memeDB Man page
mergeBSJunctions Man page
mergeMotifs Man page
mergedBSJunctions Man page
miRspeciesCodes Man page
plotExBetweenBSEs Man page Source code
plotExPosition Man page Source code
plotHostGenes Man page Source code
plotLenBSEs Man page Source code
plotLenIntrons Man page Source code
plotMiR Man page Source code
plotMotifs Man page Source code
plotTotExons Man page Source code
rearrangeMiRres Man page Source code
volcanoPlot Man page Source code
Aufiero/circRNAprofiler documentation built on July 22, 2021, 9:34 p.m.