CrispRVariants: Tools for counting and visualising mutations in a target location
Version 1.4.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHelen Lindsay [aut, cre]
Bioconductor views CRISPR DataRepresentation GeneticVariability GenomicVariation VariantDetection Visualization
Date of publicationNone
MaintainerHelen Lindsay <helen.lindsay@uzh.ch>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CrispRVariants")

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...
mergeChimeras: mergeChimeras
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...
refFromAlns: refFromAlns
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

CrisprRun Man page
CrisprRun-class Man page
CrisprSet Man page
CrisprSet-class Man page
abifToFastq Man page Source code
addClipped Man page
addClipped,GAlignments-method Man page
addCodonFrame Man page Source code
aggregateSNVs Source code
alnsToCrisprSet Source code
annotateGenePlot Man page Source code
arrangePlots Man page Source code
barplotAlleleFreqs Man page
barplotAlleleFreqs,CrisprSet-method Man page
barplotAlleleFreqs,matrix-method Man page
checkForPaired Source code
checkReadsToTargets Source code
classifyBySize Source code
collapsePairs Man page Source code
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
dispatchDots Man page Source code
excludeFromBam Man page Source code
excludeFromBamByName Source code
excludeFromBamByRange Source code
findChimeras Man page Source code
findSNVs Man page
findSNVs,CrisprSet-method Man page
getChimeras Man page
getChimeras,CrisprSet-method Man page
getOverlappingGenes Source code
gol Man page
gol_clutch1 Man page
indelPercent Man page
indelPercent,GAlignments-method Man page
makeAlignmentTilePlot Man page Source code
makeGeneSegments Source code
mergeChimeras Man page Source code
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
plotAlignments,character-method Man page
plotChimeras Man page Source code
plotFreqHeatmap Man page
plotFreqHeatmap,CrisprSet-method Man page
plotFreqHeatmap,matrix-method Man page
plotVariants Man page
plotVariants,CrisprSet-method Man page
rcAlns Man page Source code
readTargetBam Man page Source code
readsByPCRPrimer Man page
readsByPCRPrimer,GAlignments,GRanges-method Man page
readsByPCRPrimer,GRanges,GRanges-method Man page
readsToTarget Man page
readsToTarget,GAlignments,GRanges-method Man page
readsToTarget,GAlignmentsList,GRanges-method Man page
readsToTarget,character,GRanges-method Man page
readsToTargets Man page
readsToTargets,GAlignmentsList,GRanges-method Man page
readsToTargets,character,GRanges-method Man page
refFromAlns Man page
refFromAlns,GAlignments,ANY-method Man page
refFromAlns,GAlignments,GRanges-method Man page
reverseCigar Man page Source code
rmMultiPCRChimera Man page
rmMultiPCRChimera,character,Hits,integer-method Man page
separateChimeras Source code
seqsToAln Man page Source code
seqsToPartialAln Source code
setDNATileColours Man page Source code
transformAlnsToLong Man page Source code
variantCounts Man page
variantCounts,CrisprSet-method Man page
writeFastq Man page Source code

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/mergeChimeras.R
R/plotAlignments.R
R/plotChimeras.R
R/plotFreqHeatmap.R
R/plotVariants.R
R/readsByPCRPrimer.R
R/refFromAlns.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/mergeChimeras.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/refFromAlns.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-refsToAln.R
tests/testthat/test-seqsToAln.R
tests/testthat/test-utils.R
vignettes
vignettes/user_guide.Rmd
CrispRVariants documentation built on May 20, 2017, 9:51 p.m.