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

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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 <helen.lindsay@uzh.ch>
License
GPL-2
Version
1.2.0

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

Files in this package

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