.explodeCigarOpCombs    .explodeCigarOpCombs
.formatVarLabels        formatVarLabels
.getAxisCoords          .getAxisCoords
.intersperse            .intersperse
.invertKeepRanges       Helper functions for selectAlnRegions
CrisprRun-class         CrisprRun class
CrisprSet-class         CrisprSet class
abifToFastq             Read a file in ab1 (Sanger) format and convert
                        to fastq
addClipped              Extrapolates mapping location from clipped,
                        aligned reads
addCodonFrame           Internal CrispRVariants function for indicating
                        codon frame on an alignment tile plot
alleles                 Get allele names
alns                    Get alignments
annotateGenePlot        Plots and annotates transcripts
arrangePlots            Arrange plots for plotVariants:CrisprSet
barplotAlleleFreqs      Plots barplots of the spectrum of variants for
                        a sample set
collapsePairs           Internal CrispRVariants function for collapsing
                        pairs with concordant indels
consensusSeqs           Get consensus sequences for variant alleles
countDeletions          Count the number of reads containing an
                        insertion or deletion
dispatchDots            dispatchDots
excludeFromBam          Removes reads from a bam file
findChimeras            Find chimeric reads
findSNVs                Find frequent SNVs
getChimeras             Get chimeric alignments
getInsertionsTable      getInsertionsTable
gol_clutch1             Variant sequences from golden clutch 1 (Burger
                        et al)
indelLabels             indelLabels
makeAlignmentTilePlot   Internal CrispRVariants function for creating
                        the plotAlignments background
mergeChimeras           mergeChimeras
mergeCrisprSets         Merge two CrisprSets
mismatchLabels          nonindelLabels
mutationEfficiency      Get mutation efficiency
narrowAlignments        Narrow a set of aligned reads to a target
                        region
plotAlignments          Plot alignments with respect to a reference
                        sequence
plotChimeras            Display a dot plot of chimeric alignments
plotFreqHeatmap         Plot a table of counts with colours indicating
                        frequency
plotVariants            Plot alignments, frequencies and location of
                        target sequence
rcAlns                  Internal CrispRVariants function for
                        determining read orientation
readTargetBam           Internal CrispRVariants function for reading
                        and filtering a bam file
readsByPCRPrimer        Finds overlaps between aligned reads and PCR
                        primers
readsToTarget           Trims reads to a target region.
refFromAlns             refFromAlns
reverseCigar            Reverses the order of operations in a cigar
                        string
rmMultiPCRChimera       Remove chimeric reads overlapping multiple
                        primers
selectOps               selectOps
seqsToAln               Creates a text alignment from a set of cigar
                        strings
setDNATileColours       Sets colours for plotting aligned DNA
                        sequences.
setMismatchTileColours
                        Sets colours for plotting mismatches in aligned
                        DNA sequences.
transformAlnsToLong     Transform data for plotting
variantCounts           Get variant counts
writeFastq              Append a sequence to a fastq file
