{
  "_id": "6a1981c3acfb0bcc41df970e",
  "Package": "TVTB",
  "Type": "Package",
  "Title": "TVTB: The VCF Tool Box",
  "Version": "1.39.0",
  "Date": "2025-08-05",
  "Authors@R": "person(\"Kevin\", \"Rue-Albrecht\", role = c(\"aut\", \"cre\"),\nemail = \"kevinrue67@gmail.com\")",
  "Description": "The package provides S4 classes and methods to filter,\nsummarise and visualise genetic variation data stored in VCF\nfiles. In particular, the package extends the FilterRules class\n(S4Vectors package) to define news classes of filter rules\napplicable to the various slots of VCF objects. Functionalities\nare integrated and demonstrated in a Shiny web-application, the\nShiny Variant Explorer (tSVE).",
  "License": "Artistic-2.0",
  "biocViews": "Software, Genetics, GeneticVariability, GenomicVariation,\nDataRepresentation, GUI, Genetics, DNASeq, WholeGenome,\nVisualization, MultipleComparison, DataImport,\nVariantAnnotation, Sequencing, Coverage, Alignment,\nSequenceMatching",
  "Collate": "utils.R tSVE.R AllClasses.R AllGenerics.R Genotypes-class.R\nTVTBparam-class.R VcfFilterRules-class.R parseCSQToGRanges.R\ncountGenos-methods.R autodetectGenotypes.R\naddCountGenos-methods.R addFrequencies-methods.R\naddOverallFrequencies-methods.R\naddPhenoLevelFrequencies-methods.R dropInfo.R readVcf-methods.R\nvariantsInSamples-methods.R vepInPhenoLevel-methods.R\nplotInfo.R pairsInfo.R show-methods.R",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/kevinrue/TVTB",
  "BugReports": "https://github.com/kevinrue/TVTB/issues",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:36 UTC",
  "RemoteUrl": "https://github.com/bioc/TVTB",
  "RemoteRef": "HEAD",
  "RemoteSha": "c77deb7c910e894acf8844311da6fcca42390faf",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 10:14:23 UTC",
    "User": "root"
  },
  "Author": "Kevin Rue-Albrecht [aut, cre]",
  "Maintainer": "Kevin Rue-Albrecht <kevinrue67@gmail.com>",
  "MD5sum": "534803fd40ebff78ab58676a0c1bdcdc",
  "_user": "bioc",
  "_type": "src",
  "_file": "TVTB_1.39.0.tar.gz",
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  "_created": "2026-05-29T10:14:23.000Z",
  "_published": "2026-05-29T12:08:35.033Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "description": "Ingénieur diplômé;\nComputational Biologist; \nSoftware engineer;\nBioconductor contributor",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_homeurl": "https://github.com/kevinrue/tvtb",
  "_realowner": "bioc",
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  "_exports": [
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    "aaf<-",
    "active",
    "active<-",
    "addCountGenos",
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    "addOverallFrequencies",
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    "alt<-",
    "append",
    "autodetectGenotypes",
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    "bp<-",
    "carrier",
    "colData",
    "colData<-",
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    "dropInfo",
    "eval",
    "evalSeparately",
    "fixed",
    "geno",
    "genos",
    "genos<-",
    "Genotypes",
    "header",
    "header<-",
    "het",
    "het<-",
    "info",
    "info<-",
    "maf",
    "maf<-",
    "mcols",
    "metadata",
    "metadata<-",
    "pairsInfo",
    "parseCSQToGRanges",
    "plotInfo",
    "ranges",
    "ranges<-",
    "readVcf",
    "ref",
    "ref<-",
    "ScanVcfParam",
    "subsetByFilter",
    "suffix",
    "svp",
    "svp<-",
    "tSVE",
    "TVTBparam",
    "type",
    "variantsInSamples",
    "VcfFilterRules",
    "VcfFixedRules",
    "VcfInfoRules",
    "VcfVepRules",
    "vep",
    "vep<-",
    "vepInPhenoLevel"
  ],
  "_help": [
    {
      "page": "TVTB-package",
      "title": "TVTB: The VCF Tool Box",
      "topics": [
        "TVTB-package"
      ]
    },
    {
      "page": "addCountGenos-methods",
      "title": "Add count of genotypes to INFO field",
      "topics": [
        "addCountGenos",
        "addCountGenos,ExpandedVCF-method",
        "addCountGenos-methods"
      ]
    },
    {
      "page": "addFrequencies-methods",
      "title": "Group-level genotypes counts and allele frequencies",
      "topics": [
        "addFrequencies",
        "addFrequencies,ExpandedVCF,character-method",
        "addFrequencies,ExpandedVCF,list-method",
        "addFrequencies,ExpandedVCF,missing-method",
        "addFrequencies-methods"
      ]
    },
    {
      "page": "addOverallFrequencies-methods",
      "title": "Overall genotypes counts and allele frequencies",
      "topics": [
        "addOverallFrequencies",
        "addOverallFrequencies,ExpandedVCF-method",
        "addOverallFrequencies-methods"
      ]
    },
    {
      "page": "addPhenoLevelFrequencies-methods",
      "title": "Genotypes and allele frequencies for a given phenotype level",
      "topics": [
        "addPhenoLevelFrequencies",
        "addPhenoLevelFrequencies,ExpandedVCF-method",
        "addPhenoLevelFrequencies-methods"
      ]
    },
    {
      "page": "autodetectGenotypes",
      "title": "Define genotypes in the TVTBparam metadata slot",
      "topics": [
        "autodetectGenotypes",
        "autodetectGenotypes,VCF-method",
        "autodetectGenotypes-methods"
      ]
    },
    {
      "page": "countGenos-methods",
      "title": "Count occurences of genotypes",
      "topics": [
        "countGenos",
        "countGenos,ExpandedVCF-method",
        "countGenos-methods"
      ]
    },
    {
      "page": "dropInfo-methods",
      "title": "Remove INFO keys from VCF objects",
      "topics": [
        "dropInfo",
        "dropInfo,VCF-method",
        "dropInfo-methods"
      ]
    },
    {
      "page": "Genotypes-class",
      "title": "Genotypes class objects",
      "topics": [
        "alt,Genotypes-method",
        "alt<-,Genotypes,character-method",
        "carrier",
        "carrier,Genotypes-method",
        "class:Genotypes",
        "genos",
        "genos,Genotypes-method",
        "Genotypes",
        "Genotypes-class",
        "Genotypes-methods",
        "het",
        "het,Genotypes-method",
        "het<-",
        "het<-,Genotypes,character-method",
        "initialize,Genotypes-method",
        "ref,Genotypes-method",
        "ref<-,Genotypes,character-method",
        "suffix",
        "suffix,Genotypes-method"
      ]
    },
    {
      "page": "pairsInfo-methods",
      "title": "Plot an INFO metric on a genomic axis.",
      "topics": [
        "pairsInfo",
        "pairsInfo,VCF-method",
        "pairsInfo-methods"
      ]
    },
    {
      "page": "parseCSQToGRanges",
      "title": "Parse the CSQ column of a VCF object into a GRanges object",
      "topics": [
        "parseCSQToGRanges",
        "parseCSQToGRanges,VCF-method"
      ]
    },
    {
      "page": "plotInfo-methods",
      "title": "Plot an INFO metric on a genomic axis.",
      "topics": [
        "plotInfo",
        "plotInfo,VCF-method",
        "plotInfo-methods"
      ]
    },
    {
      "page": "readVcf-methods",
      "title": "Read VCF files",
      "topics": [
        "readVcf,character,TVTBparam-method",
        "readVcf,TabixFile,TVTBparam-method"
      ]
    },
    {
      "page": "tSVE",
      "title": "The Shiny Variant Explorer (tSVE) web-application",
      "topics": [
        "tSVE"
      ]
    },
    {
      "page": "TVTBParam-class",
      "title": "TVTBparam class objects",
      "topics": [
        "aaf",
        "aaf,TVTBparam-method",
        "aaf<-",
        "aaf<-,TVTBparam,character-method",
        "alt,TVTBparam-method",
        "alt<-,TVTBparam,character-method",
        "alt<-,TVTBparam,list-method",
        "bp",
        "bp,TVTBparam-method",
        "bp<-",
        "bp<-,TVTBparam,BiocParallelParam-method",
        "carrier,TVTBparam-method",
        "class:TVTBparam",
        "genos,TVTBparam-method",
        "genos<-",
        "genos<-,TVTBparam,Genotypes-method",
        "het,TVTBparam-method",
        "het<-,TVTBparam,character-method",
        "het<-,TVTBparam,list-method",
        "initialize,TVTBparam-method",
        "maf",
        "maf,TVTBparam-method",
        "maf<-",
        "maf<-,TVTBparam,character-method",
        "ranges",
        "ranges,TVTBparam-method",
        "ranges<-",
        "ranges<-,TVTBparam,GRangesList-method",
        "ref,TVTBparam-method",
        "ref<-,TVTBparam,character-method",
        "ref<-,TVTBparam,list-method",
        "suffix,TVTBparam-method",
        "svp",
        "svp,TVTBparam-method",
        "svp<-",
        "svp<-,TVTBparam,ScanVcfParam-method",
        "TVTBparam",
        "TVTBparam-class",
        "TVTBparam-methods",
        "vep",
        "vep,TVTBparam-method",
        "vep<-",
        "vep<-,TVTBparam,character-method"
      ]
    },
    {
      "page": "variantsInSamples-methods",
      "title": "Identify variants observed in samples",
      "topics": [
        "variantsInSamples",
        "variantsInSamples,ExpandedVCF-method",
        "variantsInSamples-methods"
      ]
    },
    {
      "page": "VcfBasicRules-class",
      "title": "VCF filters class objects sub-types",
      "topics": [
        "append,VcfFixedRules,FilterRules-method",
        "append,VcfInfoRules,FilterRules-method",
        "append,VcfVepRules,FilterRules-method",
        "c,VcfFixedRules-method",
        "c,VcfInfoRules-method",
        "c,VcfVepRules-method",
        "class:VcfFixedRules",
        "class:VcfInfoRules",
        "class:VcfVepRules",
        "eval,VcfFixedRules,VCF-method",
        "eval,VcfInfoRules,VCF-method",
        "eval,VcfVepRules,VCF-method",
        "initialize,VcfFixedRules-method",
        "initialize,VcfInfoRules-method",
        "initialize,VcfVepRules-method",
        "type,FilterRules-method",
        "type,VcfFixedRules-method",
        "type,VcfInfoRules-method",
        "type,VcfVepRules-method",
        "VcfFixedRules",
        "VcfFixedRules-class",
        "VcfInfoRules",
        "VcfInfoRules-class",
        "VcfVepRules",
        "VcfVepRules-class",
        "vep,FilterRules-method",
        "vep,VcfFixedRules-method",
        "vep,VcfInfoRules-method",
        "vep,VcfVepRules-method",
        "vep<-,VcfVepRules,character-method",
        "[,VcfFixedRules,ANY,ANY-method",
        "[,VcfInfoRules,ANY,ANY-method",
        "[,VcfVepRules,ANY,ANY-method",
        "[<-,VcfFixedRules,numeric,missing,VcfFixedRules-method",
        "[<-,VcfInfoRules,numeric,missing,VcfInfoRules-method",
        "[<-,VcfVepRules,numeric,missing,VcfVepRules-method",
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        "[[,VcfInfoRules,ANY,ANY-method",
        "[[,VcfVepRules,ANY,ANY-method",
        "[[<-,VcfFixedRules,ANY,ANY-method",
        "[[<-,VcfInfoRules,ANY,ANY-method",
        "[[<-,VcfVepRules,ANY,ANY-method"
      ]
    },
    {
      "page": "VcfFilterRules-class",
      "title": "VcfFilterRules class objects",
      "topics": [
        "append,VcfFilterRules,FilterRules-method",
        "c,VcfFilterRules-method",
        "class:VcfFilterRules",
        "eval,VcfFilterRules,VCF-method",
        "initialize,VcfFilterRules-method",
        "type,VcfFilterRules-method",
        "VcfFilterRules",
        "VcfFilterRules-class",
        "vep,VcfFilterRules-method",
        "vep<-,VcfFilterRules,character-method",
        "[,VcfFilterRules,ANY,ANY,ANY-method",
        "[,VcfFilterRules,ANY,ANY,logical-method",
        "[,VcfFilterRules,ANY,ANY,missing-method",
        "[<-,VcfFilterRules,numeric,missing,VcfFilterRules-method",
        "[<-,VcfFilterRules,numeric,missing,VcfFixedRules-method",
        "[<-,VcfFilterRules,numeric,missing,VcfInfoRules-method",
        "[<-,VcfFilterRules,numeric,missing,VcfVepRules-method",
        "[[,VcfFilterRules,ANY,ANY-method",
        "[[<-,VcfFilterRules,ANY,ANY-method"
      ]
    },
    {
      "page": "vepInPhenoLevel-methods",
      "title": "VEP predictions of variants observed in samples",
      "topics": [
        "vepInPhenoLevel",
        "vepInPhenoLevel,ExpandedVCF-method",
        "vepInPhenoLevel-methods"
      ]
    }
  ],
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