API for KasperThystrup/circulaR
Characterization of circRNAs from Total RNA-seq data
| Global functions | |
|---|---|
| .onAttach | Source code |
| BSJTrack | Man page Source code |
| SJTrack | Man page Source code |
| STARlogParser | Man page |
| addFilter | Man page |
| addKnownJunctions | Man page Source code |
| addLinCounts | Man page |
| adjustAlignment | Man page |
| alignmentStats | Man page |
| annotateByOverlap | Man page Source code |
| bam.file | Man page |
| bam.file<- | Man page |
| bsReadCoverage | Man page |
| bsid2bed | Man page Source code |
| bsid2gr | Man page Source code |
| bsid2junc | Man page Source code |
| bsj.counts | Man page |
| bsj.counts<- | Man page |
| bsj.reads | Man page |
| bsj.reads<- | Man page |
| bsjExonStats | Man page |
| bsjExonStats,circExperiment-method | Man page |
| bsjExonStats,circSample-method | Man page |
| bsjStats | Man page |
| c2l.ratio | Man page |
| calcCoverage | Man page |
| categorizeBSJ | Man page Source code |
| checkChimFile | Man page Source code |
| checkInputFiles | Man page Source code |
| checkPEReads | Man page Source code |
| checkPEReads_old | Man page Source code |
| checkVariables | Man page Source code |
| chim.file | Man page |
| chim.file<- | Man page |
| cigar2covr | Man page Source code |
| circExperiment | Man page |
| circExperiment-class | Man page |
| circSample | Man page |
| circulaR | Man page |
| compareToKnownJunctions | Man page |
| constructBsId | Man page |
| constructSJDB | Man page |
| count.file | Man page |
| count.file<- | Man page |
| countSumChimFile | Man page Source code |
| determineAmbiguousHits | Man page |
| exp.mat | Man page |
| findNearest | Man page |
| firstread.firststrand | Man page |
| firstread.firststrand<- | Man page |
| gb | Man page |
| gb<- | Man page |
| generateJunctionMotifs | Man page |
| getCandidateBackspliceSites | Man page Source code |
| getKnownJunctions | Man page |
| guessPE | Man page |
| indexJunctions | Man page |
| inferExons | Man page |
| is.empty | Man page |
| junctionMotif | Man page Source code |
| junctionsToGRanges | Man page |
| knownJunctionInRepeatRegion | Man page |
| knownJunctionSites | Man page |
| label | Man page |
| label<- | Man page |
| locateSamples | Man page |
| log.file | Man page |
| log.file<- | Man page |
| lsj.counts | Man page |
| lsj.counts<- | Man page |
| name | Man page |
| name<- | Man page |
| paired.end | Man page |
| paired.end<- | Man page |
| parseCIGAR | Man page Source code |
| parseDataDir | Man page |
| path | Man page |
| plotAll | Man page Source code |
| plotBSJ | Man page Source code |
| plotBSJrepeats | Man page Source code |
| plotCoverage | Man page Source code |
| plotExonStats | Man page |
| plotSJ | Man page Source code |
| plotTxModels | Man page Source code |
| plotTxModelsOLD | Man page Source code |
| pruneChromosomes | Man page |
| readBSJdata | Man page |
| readChimFile | Man page Source code |
| readLSJdata | Man page |
| rescueAmbiguous | Man page |
| resolveReads | Man page |
| sample.id | Man page |
| sample.id<- | Man page |
| samples,circExperiment-method | Man page |
| samples<- | Man page |
| shiftAlignment | Man page Source code |
| sj.file | Man page |
| sj.file<- | Man page |
| summarizeBSJreads | Man page |
| swapStrands | Man page Source code |
| vizJunctions | Man page |
| wrapperFunction | Man page Source code |
