API for CrispRVariants
Tools for counting and visualising mutations in a target location

Global functions
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
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
checkFnamesExist Source code
checkForPaired Source code
checkReadsToTarget Source code
checkReadsToTargets Source code
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
getOverlappingGenes Source code
gol Man page
gol_clutch1 Man page
indelPercent Man page
indelPercent,GAlignments-method Man page
makeAlignmentTilePlot Man page Source code
makeGeneSegments Source code
mergeChimeras Man page Source code
mergeCrisprSets Man page
mergeCrisprSets,CrisprSet,CrisprSet-method Man page
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
separateChimeras Source code
seqsToAln Man page Source code
seqsToPartialAln Man page Source code
setDNATileColours Man page Source code
transformAlnsToLong Man page Source code
variantCounts Man page
variantCounts,CrisprSet-method Man page
writeFastq Man page Source code
CrispRVariants documentation built on Nov. 17, 2017, 10:12 a.m.