CrispRVariants: Tools for counting and visualising mutations in a target location

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CrispRVariants")
AuthorHelen Lindsay [aut, cre]
Bioconductor views CRISPR DataRepresentation GeneticVariability GenomicVariation VariantDetection Visualization
Date of publicationNone
MaintainerHelen Lindsay <helen.lindsay@uzh.ch>
LicenseGPL-2
Version1.2.0

View on Bioconductor

Man pages

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

dispatchDots: dispatchDots

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

Functions

abifToFastq Man page
addClipped Man page
addClipped,GAlignments-method Man page
addCodonFrame Man page
annotateGenePlot Man page
arrangePlots Man page
barplotAlleleFreqs Man page
barplotAlleleFreqs,CrisprSet-method Man page
barplotAlleleFreqs,matrix-method Man page
collapsePairs Man page
consensusSeqs Man page
consensusSeqs,CrisprSet-method Man page
countDeletions Man page
countDeletions,GAlignments-method Man page
countIndels Man page
countIndels,GAlignments-method Man page
countInsertions Man page
countInsertions,GAlignments-method Man page
CrisprRun Man page
CrisprRun-class Man page
CrisprSet Man page
CrisprSet-class Man page
dispatchDots Man page
excludeFromBam Man page
findChimeras Man page
findSNVs Man page
findSNVs,CrisprSet-method Man page
getChimeras Man page
getChimeras,CrisprSet-method Man page
gol Man page
gol_clutch1 Man page
indelPercent Man page
indelPercent,GAlignments-method Man page
makeAlignmentTilePlot Man page
mergeCrisprSets Man page
mergeCrisprSets,CrisprSet,CrisprSet-method Man page
mutationEfficiency Man page
mutationEfficiency,CrisprSet-method Man page
narrowAlignments Man page
narrowAlignments,GAlignments,GRanges-method Man page
plotAlignments Man page
plotAlignments,CrisprSet-method Man page
plotAlignments,DNAString-method Man page
plotChimeras Man page
plotFreqHeatmap Man page
plotFreqHeatmap,CrisprSet-method Man page
plotFreqHeatmap,matrix-method Man page
plotVariants Man page
plotVariants,CrisprSet-method Man page
rcAlns Man page
readsByPCRPrimer Man page
readsByPCRPrimer,GAlignments,GRanges-method Man page
readsByPCRPrimer,GRanges,GRanges-method Man page
readsToTarget Man page
readsToTarget,character,GRanges-method Man page
readsToTarget,GAlignments,GRanges-method Man page
readsToTarget,GAlignmentsList,GRanges-method Man page
readsToTargets Man page
readsToTargets,character,GRanges-method Man page
readsToTargets,GAlignmentsList,GRanges-method Man page
readTargetBam Man page
reverseCigar Man page
rmMultiPCRChimera Man page
rmMultiPCRChimera,character,Hits,integer-method Man page
seqsToAln Man page
setDNATileColours Man page
transformAlnsToLong Man page
variantCounts Man page
variantCounts,CrisprSet-method Man page
writeFastq Man page

Files

DESCRIPTION
NAMESPACE
R
R/CrisprRun.R R/CrisprSet.R R/abifToFastq.R R/accessors.R R/barplotAlleleFreqs.R R/crispRvariants_data.R R/excludeFromBam.R R/findChimeras.R R/initialisers.R R/plotAlignments.R R/plotChimeras.R R/plotFreqHeatmap.R R/plotVariants.R R/readsByPCRPrimer.R R/reverseCigar.R R/seqsToAln.R R/utils.R R/writeFastq.R
build
build/vignette.rds
data
data/gol_clutch1.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/user_guide.R
inst/doc/user_guide.Rmd
inst/doc/user_guide.pdf
inst/extdata
inst/extdata/Danio_rerio.Zv9.73.gol.sqlite
inst/extdata/GRCz10_81_ptena_txdb.sqlite
inst/extdata/IM2033.ab1
inst/extdata/ab1
inst/extdata/ab1/ptena
inst/extdata/ab1/ptena/phenotype
inst/extdata/ab1/ptena/phenotype/embryo1
inst/extdata/ab1/ptena/phenotype/embryo1/AB2001.ab1
inst/extdata/bam
inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam
inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam.bai
inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam.bai
inst/extdata/bed
inst/extdata/bed/guide.bed
inst/extdata/cntnap2b_test_data.fastq.gz
inst/extdata/cntnap2b_test_data_guide.bed
inst/extdata/cntnap2b_test_data_s.bam
inst/extdata/gol_F1_clutch_1_embryo_1_s.bam
inst/extdata/gol_F1_clutch_1_embryo_1_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_2_s.bam
inst/extdata/gol_F1_clutch_1_embryo_2_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_3_s.bam
inst/extdata/gol_F1_clutch_1_embryo_3_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_4_s.bam
inst/extdata/gol_F1_clutch_1_embryo_4_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_5_s.bam
inst/extdata/gol_F1_clutch_1_embryo_5_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_6_s.bam
inst/extdata/gol_F1_clutch_1_embryo_6_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_7_s.bam
inst/extdata/gol_F1_clutch_1_embryo_7_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_8_s.bam
inst/extdata/gol_F1_clutch_1_embryo_8_s.bam.bai
inst/extdata/gol_F1_clutch_2_embryo_4_s.bam
inst/extdata/gol_F1_clutch_2_embryo_4_s.bam.bai
inst/extdata/gol_F1_metadata.txt
inst/extdata/gol_F1_metadata_small.txt
inst/extdata/metadata
inst/extdata/metadata/metadata.xls
inst/extdata/ptena_GRCHz10_ref.rda
inst/extdata/wtx_Sanger.png
man
man/CrisprRun-class.Rd man/CrisprSet-class.Rd man/abifToFastq.Rd man/addClipped.Rd man/addCodonFrame.Rd man/annotateGenePlot.Rd man/arrangePlots.Rd man/barplotAlleleFreqs.Rd man/collapsePairs.Rd man/consensusSeqs.Rd man/dispatchDots.Rd man/excludeFromBam.Rd man/findChimeras.Rd man/findSNVs.Rd man/getChimeras.Rd man/gol_clutch1.Rd man/indelCounts.Rd man/makeAlignmentTilePlot.Rd man/mergeCrisprSets.Rd man/mutationEfficiency.Rd man/narrowAlignments.Rd man/plotAlignments.Rd man/plotChimeras.Rd man/plotFreqHeatmap.Rd man/plotVariants.Rd man/rcAlns.Rd man/readTargetBam.Rd man/readsByPCRPrimer.Rd man/readsToTarget.Rd man/reverseCigar.Rd man/rmMultiPCRChimera.Rd man/seqsToAln.Rd man/setDNATileColours.Rd man/transformAlnsToLong.Rd man/variantCounts.Rd man/writeFastq.Rd
readme.Rmd
readme.html
readme.md
tests
tests/testthat
tests/testthat.R tests/testthat/test-accessors.R tests/testthat/test-annotate-plot.R tests/testthat/test-initialisers.R tests/testthat/test-narrowAlignments.R tests/testthat/test-plotAlignments.R tests/testthat/test-seqsToAln.R tests/testthat/test-utils.R
vignettes
vignettes/user_guide.Rmd

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