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.

AuthorHelen Lindsay [aut, cre]
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.