Man pages for CrispRVariants
Tools for counting and visualising mutations in a target location

abifToFastqRead a file in ab1 (Sanger) format and convert to fastq
addClippedExtrapolates mapping location from clipped, aligned reads
addCodonFrameInternal CrispRVariants function for indicating codon frame...
alnsGet alignments
annotateGenePlotPlots and annotates transcripts
arrangePlotsArrange plots for plotVariants:CrisprSet
barplotAlleleFreqsPlots barplots of the spectrum of variants for a sample set
collapsePairsInternal CrispRVariants function for collapsing pairs with...
consensusSeqsGet consensus sequences for variant alleles
CrisprRun-classCrisprRun class
CrisprSet-classCrisprSet class
dispatchDotsdispatchDots
excludeFromBamRemoves reads from a bam file
findChimerasFind chimeric reads
findSNVsFind frequent SNVs
getChimerasGet chimeric alignments
gol_clutch1Variant sequences from golden clutch 1 (Burger et al)
indelCountsCount the number of reads containing an insertion or deletion
makeAlignmentTilePlotInternal CrispRVariants function for creating the...
mergeChimerasmergeChimeras
mergeCrisprSetsMerge two CrisprSets
mutationEfficiencyGet mutation efficiency
narrowAlignmentsNarrow a set of aligned reads to a target region
plotAlignmentsPlot alignments with respect to a reference sequence
plotChimerasDisplay a dot plot of chimeric alignments
plotFreqHeatmapPlot a table of counts with colours indicating frequency
plotVariantsPlot alignments, frequencies and location of target sequence
rcAlnsInternal CrispRVariants function for determining read...
readsByPCRPrimerFinds overlaps between aligned reads and PCR primers
readsToTargetTrims reads to a target region.
readTargetBamInternal CrispRVariants function for reading and filtering a...
refFromAlnsrefFromAlns
reverseCigarReverses the order of operations in a cigar string
rmMultiPCRChimeraRemove chimeric reads overlapping multiple primers
seqsToAlnCreates a text alignment from a set of cigar strings
seqsToPartialAlnseqsToPartialAln
setDNATileColoursSets colours for plotting aligned DNA sequences.
transformAlnsToLongTransform data for plotting
variantCountsGet variant counts
writeFastqAppend a sequence to a fastq file
CrispRVariants documentation built on Nov. 17, 2017, 10:12 a.m.