API for Rariant
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
| Global functions | |
|---|---|
| .combineCalls | Source code |
| .wilsonScore | Source code |
| Rariant | Man page |
| Rariant-package | Man page |
| acCi | Man page Source code |
| acCi4 | Source code |
| baseFillScale | Man page Source code |
| binGRanges | Source code |
| binomTestPval | Source code |
| blogit | Source code |
| callConsensus | Man page Source code |
| call_base | Source code |
| checkCalls | Source code |
| ciAdjustLevel | Man page Source code |
| ciCovers | Man page Source code |
| ciOutside | Man page Source code |
| ciOverlap | Man page Source code |
| ciWidth | Man page Source code |
| classifyEvent | Source code |
| comparativeMismatch | Source code |
| coverageProbability | Man page Source code |
| df2gr | Source code |
| dna_bases | Source code |
| ds2int | Source code |
| eventFillScale | Man page Source code |
| evidenceHeatmap | Man page Source code |
| exampleCalls | Source code |
| feTest | Man page Source code |
| filterCalls | Man page Source code |
| findCalls | Man page Source code |
| gr2df | Source code |
| gr2pos | Man page Source code |
| gr2vr | Source code |
| grDensity | Source code |
| ind2base | Source code |
| mat2ind | Source code |
| mergeCalls | Man page Source code |
| mismatchCount | Man page Source code |
| mismatchUtils | Man page |
| nhsCi | Man page Source code |
| nmTest | Man page Source code |
| nmTestOld | Source code |
| plotAbundanceShift | Man page |
| plotCIs | Man page |
| plotConfidenceIntervals | Man page |
| plotRates | Source code |
| pos2gr | Man page Source code |
| propCIs | Man page |
| propTests | Man page |
| rariant | Man page |
| rariant,BamFile,BamFile,GRanges-method | Man page |
| rariant,array,array,GRanges-method | Man page |
| rariant,character,character,GRanges-method | Man page |
| rariant-methods | Man page |
| rariantFromBam | Source code |
| rariantFromMatrix | Source code |
| rariantInspect | Man page Source code |
| rariantStandalone | Man page Source code |
| rateFillScale | Man page Source code |
| rdSimulate | Source code |
| readRariant | Man page Source code |
| reevalSites | Source code |
| scoreTest | Man page Source code |
| selectStrand | Man page Source code |
| seqDepth | Man page Source code |
| splitSample | Man page |
| splitSampleBinom | Man page Source code |
| str_capture_matrix | Source code |
| tallyBamRegion | Man page Source code |
| tallyPlot | Man page Source code |
| updateCalls | Man page Source code |
| verdictColorScale | Man page Source code |
| vr2gr | Source code |
| writeRariant | Man page Source code |
| yesNoMaybe | Man page Source code |
