{
  "_id": "6ae744241e2c7b3a4f52fea0",
  "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": "2026-11-01 12:55:34 UTC",
    "User": "root"
  },
  "Author": "Jean-Philippe Fortin [aut, cre]",
  "Maintainer": "Jean-Philippe Fortin <fortin946@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "crisprBase_1.17.0.tar.gz",
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  "_expires": "2027-02-09T13:52:34.000Z",
  "_created": "2026-11-01T12:55:34.000Z",
  "_published": "2026-11-01T13:52:36.454Z",
  "_upstream": "https://github.com/bioc/crisprBase",
  "_status": "success",
  "_maintainer": {
    "name": "Jean-Philippe Fortin",
    "email": "fortin946@gmail.com",
    "login": "jfortin1",
    "bluesky": "@jp-fortin.bsky.social",
    "linkedin": "in/jean-philippe-fortin-98a68a47",
    "description": "Freelancer | Father of the @crisprVerse ",
    "uuid": 2328424
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      {
        "key": "crisprBase::generic:motifLength",
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      {
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    "extra/NEWS.txt",
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    "LICENSE"
  ],
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  "_realowner": "bioc",
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  "_exports": [
    "annotateMismatches",
    "BaseEditor",
    "baseEditorName",
    "baseEditorName<-",
    "CrisprNickase",
    "CrisprNuclease",
    "cutSites",
    "editingStrand",
    "editingStrand<-",
    "editingWeights",
    "extractPamFromTarget",
    "extractProtospacerFromTarget",
    "getAvailableCrisprNucleases",
    "getCutSiteFromPamSite",
    "getCutSiteRanges",
    "getEditingSiteFromPamSite",
    "getPamRanges",
    "getProtospacerRanges",
    "getTargetRanges",
    "hasSpacerGap",
    "isCutting",
    "isDnase",
    "isRnase",
    "metadata",
    "metadata<-",
    "motifLength",
    "motifs",
    "Nickase",
    "nickaseName",
    "nickaseName<-",
    "nickingStrand",
    "nickingStrand<-",
    "Nuclease",
    "nucleaseName",
    "nucleaseName<-",
    "pamIndices",
    "pamLength",
    "pams",
    "pamSide",
    "pamSide<-",
    "plotEditingWeights",
    "prototypeSequence",
    "setEditingWeights",
    "show",
    "spacerGap",
    "spacerGap<-",
    "spacerIndices",
    "spacerLength",
    "spacerLength<-",
    "targetLength",
    "targetType",
    "targetType<-",
    "weights",
    "weights<-"
  ],
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      "title": "AsCas12a CrisprNuclease object",
      "object": "AsCas12a",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "BE4max",
      "title": "BE4max BaseEditor object",
      "object": "BE4max",
      "class": [
        "BaseEditor"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "CasRx",
      "title": "CasRx CrisprNuclease object",
      "object": "CasRx",
      "class": [
        "CrisprNuclease"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Csm",
      "title": "Csm CrisprNuclease object",
      "object": "Csm",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "enAsCas12a",
      "title": "enAsCas12a CrisprNuclease object",
      "object": "enAsCas12a",
      "class": [
        "CrisprNuclease"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MAD7",
      "title": "MAD7 CrisprNuclease object",
      "object": "MAD7",
      "class": [
        "CrisprNuclease"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "restrictionEnzymes",
      "title": "List of Nuclease objects representing common restriction enzymes",
      "object": "restrictionEnzymes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SaCas9",
      "title": "SaCas9 CrisprNuclease object",
      "object": "SaCas9",
      "class": [
        "CrisprNuclease"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SpCas9",
      "title": "SpCas9 CrisprNuclease object",
      "object": "SpCas9",
      "class": [
        "CrisprNuclease"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SpG",
      "title": "SpG CrisprNuclease object",
      "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",
        "pamSide",
        "pamSide,CrisprNuclease-method",
        "pamSide<-",
        "pamSide<-,CrisprNuclease-method",
        "prototypeSequence",
        "prototypeSequence,CrisprNuclease-method",
        "show,CrisprNuclease-method",
        "spacerGap",
        "spacerGap,CrisprNuclease-method",
        "spacerGap<-",
        "spacerGap<-,CrisprNuclease-method",
        "spacerIndices",
        "spacerIndices,CrisprNuclease-method",
        "spacerLength",
        "spacerLength,CrisprNuclease-method",
        "spacerLength<-",
        "spacerLength<-,CrisprNuclease-method",
        "targetLength",
        "targetLength,CrisprNuclease-method"
      ]
    },
    {
      "page": "SpCas9",
      "title": "SpCas9 CrisprNuclease object",
      "topics": [
        "SpCas9"
      ]
    },
    {
      "page": "SpG",
      "title": "SpG CrisprNuclease object",
      "topics": [
        "SpG"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/crisprBase/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "Biostrings",
    "cli",
    "crayon",
    "generics",
    "GenomicRanges",
    "glue",
    "IRanges",
    "lifecycle",
    "magrittr",
    "rlang",
    "S4Vectors",
    "Seqinfo",
    "stringi",
    "stringr",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "crisprBase.Rmd",
      "filename": "crisprBase.html",
      "title": "Base functions and classes for CRISPR gRNA design",
      "author": "Jean-Philippe Fortin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Installation",
        "Software requirements",
        "OS Requirements",
        "Getting started",
        "Nuclease class",
        "Examples",
        "Accessor functions",
        "CrisprNuclease class",
        "CrisprNuclease objects provided in CrisprBase",
        "CRISPR arithmetics",
        "CRISPR terminology",
        "Cut site",
        "Obtaining spacer and PAM sequences from target sequences",
        "Obtaining genomic coordinates of protospacer sequences using PAM site coordinates",
        "BaseEditor class",
        "CrisprNickase class",
        "RNA-targeting nucleases",
        "Additional notes",
        "dCas9 and other \"dead\" nucleases",
        "License",
        "Reproducibility",
        "References"
      ],
      "created": "2021-09-21 19:38:18",
      "modified": "2025-10-25 21:14:56",
      "commits": 18
    }
  ],
  "_score": 7.248267603534647,
  "_indexed": true,
  "_nocasepkg": "crisprbase",
  "_universes": [
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    "jfortin1",
    "crisprverse"
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