{ "_id": "6a1fded1b401979e73438e1a", "Package": "crisprBase", "Version": "1.17.0", "Date": "2025-10-27", "Title": "Base functions and classes for CRISPR gRNA design", "Authors@R": "person(\"Jean-Philippe\", \"Fortin\", email = \"fortin946@gmail.com\", role = c(\"aut\", \"cre\"))", "biocViews": "CRISPR, FunctionalGenomics", "Description": "Provides S4 classes for general nucleases, CRISPR\nnucleases, CRISPR nickases, and base editors.Several\nCRISPR-specific genome arithmetic functions are implemented to\nhelp extract genomic coordinates of spacer and protospacer\nsequences. Commonly-used CRISPR nuclease objects are provided\nthat can be readily used in other packages. Both DNA- and\nRNA-targeting nucleases are supported.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "BugReports": "https://github.com/crisprVerse/crisprBase/issues", "URL": "https://github.com/crisprVerse/crisprBase", "Collate": "'AllGenerics.R' 'rebase.R' 'Nuclease-class.R'\n'Nickase-class.R' 'CrisprNuclease-class.R'\n'CrisprNickase-class.R' 'BaseEditor-class.R' 'arithmetics.R'\n'data.R' 'utils.R' 'converters.R' 'annotateMismatches.R'", "LazyData": "true", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:37 UTC", "RemoteUrl": "https://github.com/bioc/crisprBase", "RemoteRef": "HEAD", "RemoteSha": "f896dbd50ae7cbefbee2cda645cd814a12ded936", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 07:53:46 UTC", "User": "root" }, "Author": "Jean-Philippe Fortin [aut, cre]", "Maintainer": "Jean-Philippe Fortin ", "MD5sum": 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"object": "SpG", "class": [ "CrisprNuclease" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "annotateMismatches", "title": "Annotate mismatches between spacer and protospacer sequences", "topics": [ "annotateMismatches" ] }, { "page": "AsCas12a", "title": "AsCas12a CrisprNuclease object", "topics": [ "AsCas12a" ] }, { "page": "BaseEditor-class", "title": "An S4 class to represent a base editor", "topics": [ "BaseEditor", "BaseEditor-class", "baseEditorName", "baseEditorName,BaseEditor-method", "baseEditorName<-", "baseEditorName<-,BaseEditor-method", "editingStrand", "editingStrand,BaseEditor-method", "editingStrand<-", "editingStrand<-,BaseEditor-method", "editingWeights", "editingWeights,BaseEditor-method", "setEditingWeights", "show,BaseEditor-method" ] }, { "page": "BE4max", "title": "BE4max BaseEditor object", "topics": [ "BE4max" ] }, { "page": "CasRx", "title": "CasRx CrisprNuclease object", "topics": [ "CasRx" ] }, { "page": "CrisprNickase-class", "title": "An S4 class to represent a CRISPR nickase.", "topics": [ "CrisprNickase", "CrisprNickase-class", "hasSpacerGap,CrisprNickase-method", "pamIndices,CrisprNickase-method", "pamLength,CrisprNickase-method", "pams,CrisprNickase-method", "pamSide,CrisprNickase-method", "pamSide<-,CrisprNickase-method", "prototypeSequence,CrisprNickase-method", "show,CrisprNickase-method", "spacerGap,CrisprNickase-method", "spacerGap<-,CrisprNickase-method", "spacerIndices,CrisprNickase-method", "spacerLength,CrisprNickase-method", "spacerLength<-,CrisprNickase-method", "targetLength,CrisprNickase-method" ] }, { "page": "Csm", "title": "Csm CrisprNuclease object", "topics": [ "Csm" ] }, { "page": "enAsCas12a", "title": "enAsCas12a CrisprNuclease object", "topics": [ "enAsCas12a" ] }, { "page": "extractPamFromTarget", "title": "Extract PAM sequences from target sequences", "topics": [ "extractPamFromTarget" ] }, { "page": "extractProtospacerFromTarget", "title": "Extract protospacer sequences from target sequences", "topics": [ "extractProtospacerFromTarget" ] }, { "page": "getAvailableCrisprNucleases", "title": "Return list of available CrisprNuclease objects in crisprBase", "topics": [ "getAvailableCrisprNucleases" ] }, { "page": "getCutSiteFromPamSite", "title": "Return cut site coordinates from PAM site coordinates", "topics": [ "getCutSiteFromPamSite" ] }, { "page": "getCutSiteRanges", "title": "Construct a cut site GRanges from a list of PAM sites", "topics": [ "getCutSiteRanges" ] }, { "page": "getEditingSiteFromPamSite", "title": "Return optimal editing site coordinates from PAM site coordinates", "topics": [ "getEditingSiteFromPamSite" ] }, { "page": "getPamRanges", "title": "Construct a PAM GRanges from a list of PAM sites", "topics": [ "getPamRanges" ] }, { "page": "getProtospacerRanges", "title": "Construct a protospacer GRanges from a list of PAM sites", "topics": [ "getProtospacerRanges" ] }, { "page": "getTargetRanges", "title": "Construct a target GRanges from a list of PAM sites", "topics": [ "getTargetRanges" ] }, { "page": "MAD7", "title": "MAD7 CrisprNuclease object", "topics": [ "MAD7" ] }, { "page": "Nuclease-class", "title": "An S4 class to represent a nuclease.", "topics": [ "cutSites", "cutSites,Nuclease-method", "isCutting", "isCutting,Nuclease-method", "isDnase", "isDnase,Nuclease-method", "isRnase", "isRnase,Nuclease-method", "motifLength", "motifLength,Nuclease-method", "motifs", "motifs,Nuclease-method", "Nuclease", "Nuclease-class", "nucleaseName", "nucleaseName,Nuclease-method", "nucleaseName<-", "nucleaseName<-,Nuclease-method", "show,Nuclease-method", "targetType", "targetType,Nuclease-method", "targetType<-", "targetType<-,Nuclease-method", "weights", "weights,Nuclease-method", "weights<-", "weights<-,Nuclease-method" ] }, { "page": "Nickase-class", "title": "An S4 class to represent a nickase", "topics": [ "cutSites,Nickase-method", "isCutting,Nickase-method", "motifLength,Nickase-method", "motifs,Nickase-method", "Nickase", "Nickase-class", "nickaseName", "nickaseName,Nickase-method", "nickaseName<-", "nickaseName<-,Nickase-method", "nickingStrand", "nickingStrand,Nickase-method", "nickingStrand<-", "nickingStrand<-,Nickase-method", "show,Nickase-method", "weights,Nickase-method", "weights<-,Nickase-method" ] }, { "page": "plotEditingWeights", "title": "Quick plot to visualize editing weights", "topics": [ "plotEditingWeights" ] }, { "page": "restrictionEnzymes", "title": "List of Nuclease objects representing common restriction enzymes", "topics": [ "restrictionEnzymes" ] }, { "page": "SaCas9", "title": "SaCas9 CrisprNuclease object", "topics": [ "SaCas9" ] }, { "page": "CrisprNuclease-class", "title": "An S4 class to represent a CRISPR nuclease.", "topics": [ "CrisprNuclease", "CrisprNuclease-class", "hasSpacerGap", "hasSpacerGap,CrisprNuclease-method", "pamIndices", "pamIndices,CrisprNuclease-method", "pamLength", "pamLength,CrisprNuclease-method", "pams", "pams,CrisprNuclease-method", 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