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CrispRVariants (version 1.0.2)

Tools for counting and visualising mutations in a target location

Description

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.

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Version

Version

1.0.2

License

GPL-2

Maintainer

Helen Lindsay

Last Published

February 15th, 2017

Functions in CrispRVariants (1.0.2)

findSNVs

Find frequent SNVs
findChimeras

Find chimeric reads
rcAlns

Internal CrispRVariants function for deciding whether to reverse complement aligned reads
readsByPCRPrimer

Finds overlaps between aligned reads and PCR primers
CrisprRun-class

CrisprRun class
CrisprSet-class

CrisprSet class
mutationEfficiency

Get mutation efficiency
narrowAlignments

Narrow a set of aligned reads to a target region
setDNATileColours

Sets colours for plotting aligned DNA sequences.
seqsToAln

Creates a text alignment from a set of cigar strings
barplotAlleleFreqs

Plots barplots of the spectrum of variants for a sample set
collapsePairs

Internal CrispRVariants function for collapsing pairs with concordant indels
getChimeras

Get chimeric alignments
plotFreqHeatmap

Plot a table of counts with colours indicating frequency
gol_clutch1

Variant sequences from golden clutch 1 (Burger et al)
plotVariants

Plot alignments, frequencies and location of target sequence
abifToFastq

Read a file in ab1 (Sanger) format and convert to fastq
addClipped

Extrapolates mapping location from clipped, aligned reads
transformAlnsToLong

Transform data for plotting
variantCounts

Get variant counts
dispatchDots

dispatchDots
plotAlignments

Plot alignments with respect to a reference sequence
excludeFromBam

Removes reads from a bam file
plotChimeras

Display a dot plot of chimeric alignments
readsToTarget

Trims reads to a target region.
readTargetBam

Internal CrispRVariants function for reading and filtering a bam file
writeFastq

Append a sequence to a fastq file
countDeletions

Count the number of reads containing an insertion or deletion
annotateGenePlot

Plots and annotates transcripts
arrangePlots

Arrange plots for plotVariants:CrisprSet
mergeCrisprSets

Merge two CrisprSets
reverseCigar

Reverses the order of operations in a cigar string
rmMultiPCRChimera

Remove chimeric reads overlapping multiple primers