CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
|Author||Helen Lindsay [aut, cre]|
|Date of publication||None|
|Maintainer||Helen Lindsay <email@example.com>|
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...
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...
consensusSeqs: Get consensus sequences for variant alleles
CrisprRun-class: CrisprRun class
CrisprSet-class: CrisprSet class
excludeFromBam: Removes reads from a bam file
findChimeras: Find chimeric reads
findSNVs: Find frequent SNVs
getChimeras: Get chimeric alignments
gol_clutch1: Variant sequences from golden clutch 1 (Burger et al)
indelCounts: Count the number of reads containing an insertion or deletion
makeAlignmentTilePlot: Internal CrispRVariants function for creating the...
mergeCrisprSets: Merge two CrisprSets
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...
readsByPCRPrimer: Finds overlaps between aligned reads and PCR primers
readsToTarget: Trims reads to a target region.
readTargetBam: Internal CrispRVariants function for reading and filtering a...
reverseCigar: Reverses the order of operations in a cigar string
rmMultiPCRChimera: 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
writeFastq: Append a sequence to a fastq file