Introduction | Quickstart | Case study: Analysis of ptena mutant spectrum in zebrafish | Convert AB1-format Sanger sequences to FASTQ | Map the FASTQ reads | List the BAM files | Create the target location and reference sequence | Note for Windows and Galaxy Users | Creating a CrisprSet | Creating summary plots of variants | Calculating the mutation efficiency | Get consensus alleles | Plot chimeric alignments | Choosing the strand for display | Multiple guides | Changing the appearance of plots | Filtering data in plotVariants | plotAlignments | Insertion symbols | Whitespace between rows | Box around guide | Text sizes | Box around PAM | Add a codon frame | Other modifications | plotFreqHeatmap | Plotting allele proportions | Changing the header | Heatmap colours | Changing colours of x-labels | Controlling the appearance of the legend | Further customisation | barplotAlleleFreqs | Using CrispRVariants plotting functions independently | Plot the reference sequence | Note about handling of large deletions | Session Info
Package: CrispRVariants 1.41.0
Helen Lindsay
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.
Authors:
CrispRVariants_1.41.0.tar.gz
CrispRVariants_1.41.0.zip(r-4.7)CrispRVariants_1.41.0.zip(r-4.6)CrispRVariants_1.41.0.zip(r-4.5)
CrispRVariants_1.41.0.tgz(r-4.6-any)CrispRVariants_1.41.0.tgz(r-4.5-any)
CrispRVariants_1.41.0.tar.gz(r-4.7-any)CrispRVariants_1.41.0.tar.gz(r-4.6-any)
CrispRVariants_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CrispRVariants/json (API)
| # Install 'CrispRVariants' in R: |
| install.packages('CrispRVariants', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- gol - Variant sequences from golden clutch 1
On BioConductor:CrispRVariants-1.41.0(bioc 3.24)CrispRVariants-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologycrisprgenomicvariationvariantdetectiongeneticvariabilitydatarepresentationvisualizationsequencing
Last updated from:9e4cfc201c. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 214 | ||
| linux-devel-x86_64 | WARNING | 406 | ||
| source / vignettes | OK | 349 | ||
| linux-release-x86_64 | WARNING | 445 | ||
| macos-release-arm64 | WARNING | 213 | ||
| macos-oldrel-arm64 | WARNING | 215 | ||
| windows-devel | WARNING | 340 | ||
| windows-release | WARNING | 317 | ||
| windows-oldrel | WARNING | 317 | ||
| wasm-release | OK | 199 |
Exports:abifToFastqallelesalnsbarplotAlleleFreqsconsensusSeqscountDeletionscountIndelscountInsertionsCrisprRunCrisprSetfindChimerasfindSNVsgetChimerasindelPercentmergeCrisprSetsmutationEfficiencynarrowAlignmentsplotAlignmentsplotChimerasplotFreqHeatmapplotVariantsreadsByPCRPrimerreadsToTargetreadsToTargetsrefFromAlnsvariantCounts
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplyrpngR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| .explodeCigarOpCombs | .explodeCigarOpCombs |
| formatVarLabels | .findMismatches .formatVarLabels |
| .getAxisCoords | .getAxisCoords |
| .intersperse | .intersperse |
| Helper functions for selectAlnRegions | .adjustRelativeInsLocs .checkRelativeLocs .invertKeepRanges .offsetIndices |
| Read a file in ab1 (Sanger) format and convert to fastq | abifToFastq |
| Extrapolates mapping location from clipped, aligned reads | addClipped addClipped,GAlignments-method |
| Internal CrispRVariants function for indicating codon frame on an alignment tile plot | addCodonFrame |
| Get allele names | alleles alleles,CrisprSet-method |
| Get alignments | alns alns,CrisprSet-method |
| Plots and annotates transcripts | annotateGenePlot |
| Arrange plots for plotVariants:CrisprSet | arrangePlots |
| Plots barplots of the spectrum of variants for a sample set | barplotAlleleFreqs barplotAlleleFreqs,CrisprSet-method barplotAlleleFreqs,matrix-method |
| Internal CrispRVariants function for collapsing pairs with concordant indels | collapsePairs |
| Get consensus sequences for variant alleles | consensusSeqs consensusSeqs,CrisprSet-method |
| Count the number of reads containing an insertion or deletion | countDeletions countDeletions,GAlignments-method countIndels countIndels,GAlignments-method countInsertions countInsertions,GAlignments-method indelPercent indelPercent,GAlignments-method |
| CrisprRun class | CrisprRun CrisprRun-class |
| CrisprSet class | CrisprSet CrisprSet-class |
| dispatchDots | dispatchDots |
| Removes reads from a bam file | excludeFromBam |
| Find chimeric reads | findChimeras |
| Find frequent SNVs | findSNVs findSNVs,CrisprSet-method |
| Get chimeric alignments | getChimeras getChimeras,CrisprSet-method |
| getInsertionsTable | getInsertionsTable |
| Variant sequences from golden clutch 1 (Burger et al) | gol gol_clutch1 |
| indelLabels | indelLabels |
| Internal CrispRVariants function for creating the plotAlignments background | makeAlignmentTilePlot |
| mergeChimeras | mergeChimeras |
| Merge two CrisprSets | mergeCrisprSets mergeCrisprSets,CrisprSet,CrisprSet-method |
| nonindelLabels | mismatchLabels |
| Get mutation efficiency | mutationEfficiency mutationEfficiency,CrisprSet-method |
| Narrow a set of aligned reads to a target region | narrowAlignments narrowAlignments,GAlignments,GRanges-method |
| Plot alignments with respect to a reference sequence | plotAlignments plotAlignments,character-method plotAlignments,CrisprSet-method plotAlignments,DNAString-method |
| Display a dot plot of chimeric alignments | plotChimeras |
| Plot a table of counts with colours indicating frequency | plotFreqHeatmap plotFreqHeatmap,CrisprSet-method plotFreqHeatmap,matrix-method |
| Plot alignments, frequencies and location of target sequence | plotVariants plotVariants,CrisprSet-method |
| Internal CrispRVariants function for determining read orientation | rcAlns |
| Finds overlaps between aligned reads and PCR primers | readsByPCRPrimer readsByPCRPrimer,GAlignments,GRanges-method readsByPCRPrimer,GRanges,GRanges-method |
| Trims reads to a target region. | readsToTarget readsToTarget,character,GRanges-method readsToTarget,GAlignments,GRanges-method readsToTarget,GAlignmentsList,GRanges-method readsToTargets readsToTargets,character,GRanges-method readsToTargets,GAlignmentsList,GRanges-method |
| Internal CrispRVariants function for reading and filtering a bam file | readTargetBam |
| refFromAlns | refFromAlns refFromAlns,GAlignments,ANY-method refFromAlns,GAlignments,GRanges-method |
| Reverses the order of operations in a cigar string | reverseCigar |
| Remove chimeric reads overlapping multiple primers | rmMultiPCRChimera rmMultiPCRChimera,character,Hits,integer-method |
| selectOps | selectOps selectOps,character-method |
| Creates a text alignment from a set of cigar strings | selectAlnRegions seqsToAln |
| Sets colours for plotting aligned DNA sequences. | setDNATileColours |
| Sets colours for plotting mismatches in aligned DNA sequences. | setMismatchTileColours |
| Transform data for plotting | transformAlnsToLong |
| Get variant counts | variantCounts variantCounts,CrisprSet-method |
| Append a sequence to a fastq file | writeFastq |
