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

Global functions
.adjustRelativeInsLocs Man page
.checkRelativeLocs Man page
.explodeCigarOpCombs Man page
.findMismatches Man page
.formatVarLabels Man page
.getAxisCoords Man page
.intersperse Man page
.invertKeepRanges Man page
.offsetIndices Man page
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
adjustRelativeInsLocs 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
checkFnamesExist Source code
checkForPaired Source code
checkReadsToTarget Source code
checkReadsToTargets Source code
checkRelativeLocs 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
createCrisprRun Source code
defaultCigarLabels Source code
dispatchDots Man page Source code
excludeFromBam Man page Source code
excludeFromBamByName Source code
excludeFromBamByRange Source code
explodeCigarOpCombs Source code
findChimeras Man page Source code
findMismatches Source code
findSNVs Man page
findSNVs,CrisprSet-method Man page
formatVarLabels Source code
getAxisCoords Source code
getChimeras Man page
getChimeras,CrisprSet-method Man page
getDNAColours Source code
getInsertionsTable Man page Source code
getOverlappingGenes 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
makeGeneSegments 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
ntersperse Source code
nvertKeepRanges Source code
offsetIndices Source code
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
resolveRefStrand Source code
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
transformAlnsToLong Man page Source code
variantCounts Man page
variantCounts,CrisprSet-method Man page
writeFastq Man page Source code
CrispRVariants documentation built on May 2, 2018, 2:36 a.m.