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