{ "_id": "6a1ad67a1d7bb097a09e5b85", "Package": "CrispRVariants", "Type": "Package", "Title": "Tools for counting and visualising mutations in a target\nlocation", "Version": "1.41.0", "Authors@R": "c(person(given = \"Helen\", family = \"Lindsay\", role = c(\"aut\", \"cre\"), email =\n\"helen.lindsay@chuv.ch\"))", "Author": "Helen Lindsay [aut, cre]", "Description": "CrispRVariants provides tools for analysing the results of\na CRISPR-Cas9 mutagenesis sequencing experiment, or other\nsequencing experiments where variants within a given region are\nof interest. These tools allow users to localize variant allele\ncombinations with respect to any genomic location (e.g. the\nCas9 cut site), plot allele combinations and calculate mutation\nrates with flexible filtering of unrelated variants.", "biocViews": "ImmunoOncology, CRISPR, GenomicVariation, VariantDetection,\nGeneticVariability, DataRepresentation, Visualization,\nSequencing", "Encoding": "UTF-8", "License": "GPL-2", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:23 UTC", "RemoteUrl": "https://github.com/bioc/CrispRVariants", "RemoteRef": "HEAD", "RemoteSha": "9e4cfc201c296c37bbfd7ad86004184a484a7a74", "Packaged": { "Date": "2026-05-30 08:48:21 UTC", "User": "root" }, "Maintainer": "Helen Lindsay ", "MD5sum": "abd266599408cd05455d86e18a1b47e0", "_user": "bioc", "_type": "src", 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"title": "Internal CrispRVariants function for collapsing pairs with concordant indels", "topics": [ "collapsePairs" ] }, { "page": "consensusSeqs", "title": "Get consensus sequences for variant alleles", "topics": [ "consensusSeqs", "consensusSeqs,CrisprSet-method" ] }, { "page": "indelCounts", "title": "Count the number of reads containing an insertion or deletion", "topics": [ "countDeletions", "countDeletions,GAlignments-method", "countIndels", "countIndels,GAlignments-method", "countInsertions", "countInsertions,GAlignments-method", "indelPercent", "indelPercent,GAlignments-method" ] }, { "page": "CrisprRun-class", "title": "CrisprRun class", "topics": [ "CrisprRun", "CrisprRun-class" ] }, { "page": "CrisprSet-class", "title": "CrisprSet class", "topics": [ "CrisprSet", "CrisprSet-class" ] }, { "page": "dispatchDots", "title": "dispatchDots", "topics": [ "dispatchDots" ] }, { "page": "excludeFromBam", "title": "Removes reads from a bam file", "topics": [ "excludeFromBam" ] }, { "page": "findChimeras", "title": "Find chimeric reads", "topics": [ "findChimeras" ] }, { "page": "findSNVs", "title": "Find frequent SNVs", "topics": [ "findSNVs", "findSNVs,CrisprSet-method" ] }, { "page": "getChimeras", "title": "Get chimeric alignments", "topics": [ "getChimeras", "getChimeras,CrisprSet-method" ] }, { "page": "getInsertionsTable", "title": "getInsertionsTable", "topics": [ "getInsertionsTable" ] }, { "page": "gol_clutch1", "title": "Variant sequences from golden clutch 1 (Burger et al)", "topics": [ "gol", "gol_clutch1" ] }, { "page": "indelLabels", "title": "indelLabels", "topics": [ "indelLabels" ] }, { "page": "makeAlignmentTilePlot", "title": "Internal CrispRVariants function for creating the plotAlignments background", "topics": [ "makeAlignmentTilePlot" ] }, { "page": "mergeChimeras", "title": "mergeChimeras", "topics": [ "mergeChimeras" ] }, { "page": "mergeCrisprSets", "title": "Merge two CrisprSets", "topics": [ "mergeCrisprSets", "mergeCrisprSets,CrisprSet,CrisprSet-method" ] }, { "page": "mismatchLabels", "title": "nonindelLabels", "topics": [ "mismatchLabels" ] }, { "page": "mutationEfficiency", "title": "Get mutation efficiency", "topics": [ "mutationEfficiency", "mutationEfficiency,CrisprSet-method" ] }, { "page": "narrowAlignments", "title": "Narrow a set of aligned reads to a target region", "topics": [ "narrowAlignments", "narrowAlignments,GAlignments,GRanges-method" ] }, { "page": "plotAlignments", "title": "Plot alignments with respect to a reference sequence", "topics": [ "plotAlignments", "plotAlignments,character-method", "plotAlignments,CrisprSet-method", "plotAlignments,DNAString-method" ] }, { "page": "plotChimeras", "title": "Display a dot plot of chimeric alignments", "topics": [ "plotChimeras" ] }, { "page": "plotFreqHeatmap", "title": "Plot a table of counts with colours indicating frequency", "topics": [ "plotFreqHeatmap", "plotFreqHeatmap,CrisprSet-method", "plotFreqHeatmap,matrix-method" ] }, { "page": "plotVariants", "title": "Plot alignments, frequencies and location of target sequence", "topics": [ "plotVariants", "plotVariants,CrisprSet-method" ] }, { "page": "rcAlns", "title": "Internal CrispRVariants function for determining read orientation", "topics": [ "rcAlns" ] }, { "page": "readsByPCRPrimer", "title": "Finds overlaps between aligned reads and PCR primers", "topics": [ "readsByPCRPrimer", "readsByPCRPrimer,GAlignments,GRanges-method", "readsByPCRPrimer,GRanges,GRanges-method" ] }, { "page": "readsToTarget", "title": "Trims reads to a target region.", "topics": [ "readsToTarget", "readsToTarget,character,GRanges-method", "readsToTarget,GAlignments,GRanges-method", "readsToTarget,GAlignmentsList,GRanges-method", "readsToTargets", "readsToTargets,character,GRanges-method", "readsToTargets,GAlignmentsList,GRanges-method" ] }, { "page": "readTargetBam", "title": "Internal CrispRVariants function for reading and filtering a bam file", "topics": [ "readTargetBam" ] 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