| .adjustRelativeInsLocs |
Man page
Source code
|
| .checkFnamesExist |
Source code
|
| .checkForPaired |
Source code
|
| .checkReadsToTarget |
Source code
|
| .checkReadsToTargets |
Source code
|
| .checkRelativeLocs |
Man page
Source code
|
| .defaultCigarLabels |
Source code
|
| .explodeCigarOpCombs |
Man page
Source code
|
| .findMismatches |
Man page
Source code
|
| .formatVarLabels |
Man page
Source code
|
| .getAxisCoords |
Man page
Source code
|
| .getDNAColours |
Source code
|
| .getOverlappingGenes |
Source code
|
| .intersperse |
Man page
Source code
|
| .invertKeepRanges |
Man page
Source code
|
| .makeGeneSegments |
Source code
|
| .offsetIndices |
Man page
Source code
|
| .resolveRefStrand |
Source code
|
| CrisprRun |
Man page
|
| CrisprRun-class |
Man page
|
| CrisprSet |
Man page
|
| CrisprSet-class |
Man page
|
| abifToFastq |
Man page
Source code
|
| addClipped |
Man page
|
| addClipped,GAlignments-method |
Man page
|
| addCodonFrame |
Man page
Source code
|
| aggregateSNVs |
Source code
|
| alleles |
Man page
|
| alleles,CrisprSet-method |
Man page
|
| alns |
Man page
|
| alns,CrisprSet-method |
Man page
|
| alnsToCrisprSet |
Source code
|
| annotateGenePlot |
Man page
Source code
|
| arrangePlots |
Man page
Source code
|
| barplotAlleleFreqs |
Man page
|
| barplotAlleleFreqs,CrisprSet-method |
Man page
|
| barplotAlleleFreqs,matrix-method |
Man page
|
| classifyBySize |
Source code
|
| collapsePairs |
Man page
Source code
|
| consensusSeqs |
Man page
|
| consensusSeqs,CrisprSet-method |
Man page
|
| countDeletions |
Man page
|
| countDeletions,GAlignments-method |
Man page
|
| countIndels |
Man page
|
| countIndels,GAlignments-method |
Man page
|
| countInsertions |
Man page
|
| countInsertions,GAlignments-method |
Man page
|
| dispatchDots |
Man page
Source code
|
| excludeFromBam |
Man page
Source code
|
| excludeFromBamByName |
Source code
|
| excludeFromBamByRange |
Source code
|
| findChimeras |
Man page
Source code
|
| findSNVs |
Man page
|
| findSNVs,CrisprSet-method |
Man page
|
| getChimeras |
Man page
|
| getChimeras,CrisprSet-method |
Man page
|
| getInsertionsTable |
Man page
Source code
|
| gol |
Man page
|
| gol_clutch1 |
Man page
|
| indelLabels |
Man page
Source code
|
| indelPercent |
Man page
|
| indelPercent,GAlignments-method |
Man page
|
| isFALSE |
Source code
|
| makeAlignmentTilePlot |
Man page
Source code
|
| matchLabels |
Source code
|
| mergeChimeras |
Man page
Source code
|
| mergeCrisprSets |
Man page
|
| mergeCrisprSets,CrisprSet,CrisprSet-method |
Man page
|
| mismatchLabels |
Man page
Source code
|
| mutationEfficiency |
Man page
|
| mutationEfficiency,CrisprSet-method |
Man page
|
| narrowAlignments |
Man page
|
| narrowAlignments,GAlignments,GRanges-method |
Man page
|
| plotAlignments |
Man page
|
| plotAlignments,CrisprSet-method |
Man page
|
| plotAlignments,DNAString-method |
Man page
|
| plotAlignments,character-method |
Man page
|
| plotChimeras |
Man page
Source code
|
| plotFreqHeatmap |
Man page
|
| plotFreqHeatmap,CrisprSet-method |
Man page
|
| plotFreqHeatmap,matrix-method |
Man page
|
| plotVariants |
Man page
|
| plotVariants,CrisprSet-method |
Man page
|
| rcAlns |
Man page
Source code
|
| readTargetBam |
Man page
Source code
|
| readsByPCRPrimer |
Man page
|
| readsByPCRPrimer,GAlignments,GRanges-method |
Man page
|
| readsByPCRPrimer,GRanges,GRanges-method |
Man page
|
| readsToTarget |
Man page
|
| readsToTarget,GAlignments,GRanges-method |
Man page
|
| readsToTarget,GAlignmentsList,GRanges-method |
Man page
|
| readsToTarget,character,GRanges-method |
Man page
|
| readsToTargets |
Man page
|
| readsToTargets,GAlignmentsList,GRanges-method |
Man page
|
| readsToTargets,character,GRanges-method |
Man page
|
| refFromAlns |
Man page
|
| refFromAlns,GAlignments,ANY-method |
Man page
|
| refFromAlns,GAlignments,GRanges-method |
Man page
|
| reverseCigar |
Man page
Source code
|
| rmMultiPCRChimera |
Man page
|
| rmMultiPCRChimera,character,Hits,integer-method |
Man page
|
| selectAlnRegions |
Man page
Source code
|
| selectOps |
Man page
|
| selectOps,character-method |
Man page
|
| separateChimeras |
Source code
|
| seqsToAln |
Man page
Source code
|
| setDNATileColours |
Man page
Source code
|
| setMismatchTileColours |
Man page
Source code
|
| splitInsertions |
Source code
|
| transformAlnsToLong |
Man page
Source code
|
| variantCounts |
Man page
|
| variantCounts,CrisprSet-method |
Man page
|
| writeFastq |
Man page
Source code
|
