API for 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 |
