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  "Title": "Filtering of coding and non-coding genetic variants",
  "Description": "Filter genetic variants using different criteria such as\ninheritance model, amino acid change consequence, minor allele\nfrequencies across human populations, splice site strength,\nconservation, etc.",
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  "Date/Publication": "2026-04-28 12:39:01 UTC",
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  "Author": "Robert Castelo [aut, cre],\nDei Martinez Elurbe [ctb],\nPau Puigdevall [ctb],\nJoan Fernandez [ctb]",
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    "bamFiles",
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    "FiveSpliceSiteVariants",
    "genePhylostrata",
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    "OMIMpresent",
    "OMIMpresent<-",
    "param",
    "readAAradicalChangeMatrix",
    "readWm",
    "reportVariants",
    "resetSamples",
    "samples",
    "samples<-",
    "sequence_variant.gSOXP",
    "show",
    "softFilterMatrix",
    "softFilterMatrix<-",
    "sog",
    "sortings",
    "sortings<-",
    "spliceSiteMatricesHuman",
    "summary",
    "ThreeSpliceSiteVariants",
    "unrelatedIndividuals",
    "upstream",
    "upstream<-",
    "variantConsequence",
    "variantConsequence<-",
    "VariantFilteringParam",
    "variantLocation",
    "variantLocation<-",
    "variantLocations",
    "variantType",
    "variantType<-",
    "width",
    "wmFilename",
    "wmLocations",
    "wmLocations<-",
    "wmName",
    "wmScore",
    "wmStrictLocations",
    "wmStrictLocations<-",
    "xLinked"
  ],
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    {
      "page": "VariantFiltering-package",
      "title": "Filtering of coding and non-coding genetic variants",
      "topics": [
        "VariantFiltering-package",
        "VariantFiltering"
      ]
    },
    {
      "page": "autosomalDominant",
      "title": "Autosomal dominant inheritance analysis",
      "topics": [
        "autosomalDominant",
        "autosomalDominant,VariantFilteringParam-method"
      ]
    },
    {
      "page": "autosomalRecessiveHeterozygous",
      "title": "Autosomal recessive inheritance analysis: Heterozygous",
      "topics": [
        "autosomalRecessiveHeterozygous",
        "autosomalRecessiveHeterozygous,VariantFilteringParam-method"
      ]
    },
    {
      "page": "autosomalRecessiveHomozygous",
      "title": "Autosomal recessive inheritance analysis: Homozygous",
      "topics": [
        "autosomalRecessiveHomozygous",
        "autosomalRecessiveHomozygous,VariantFilteringParam-method"
      ]
    },
    {
      "page": "deNovo",
      "title": "De Novo variants analysis",
      "topics": [
        "deNovo",
        "deNovo,VariantFilteringParam-method"
      ]
    },
    {
      "page": "GenePhylostrataDb-class",
      "title": "PhastConsDb class",
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        "genePhylostrata",
        "genePhylostrata,GenePhylostrataDb-method",
        "GenePhylostrataDb",
        "GenePhylostrataDb-class",
        "genePhylostratum",
        "genePhylostratum,GenePhylostrataDb,character-method",
        "genePhylostratum,GenePhylostrataDb,missing-method",
        "genePhylostratum,GenePhylostrataDb-method",
        "humanGenesPhylostrata",
        "organism,GenePhylostrataDb-method",
        "show,GenePhylostrataDb-method"
      ]
    },
    {
      "page": "readAAradicalChangeMatrix",
      "title": "Read matrix of amino acid radical changes",
      "topics": [
        "readAAradicalChangeMatrix"
      ]
    },
    {
      "page": "unrelatedIndividuals",
      "title": "Analysis designed to be applied over a group of unrelated individuals",
      "topics": [
        "unrelatedIndividuals",
        "unrelatedIndividuals,VariantFilteringParam-method"
      ]
    },
    {
      "page": "VariantFilteringParam-class",
      "title": "VariantFiltering parameter class",
      "topics": [
        "$,VariantFilteringParam-method",
        "class:VariantFilteringParam",
        "cutoffs,VariantFilteringParam-method",
        "filters,VariantFilteringParam-method",
        "names,VariantFilteringParam-method",
        "sequence_variant.gSOXP",
        "show,VariantFilteringParam-method",
        "sog,VariantFilteringParam-method",
        "spliceSiteMatricesHuman",
        "VariantFilteringParam",
        "VariantFilteringParam-class",
        "variantLocations"
      ]
    },
    {
      "page": "VariantFilteringResults-class",
      "title": "VariantFilteringResults class",
      "topics": [
        "allVariants",
        "allVariants,VariantFilteringResults-method",
        "annoGroups",
        "annoGroups,VariantFilteringResults-method",
        "bamFiles",
        "bamFiles,VariantFilteringResults-method",
        "bamFiles<-",
        "bamFiles<-,VariantFilteringResults,BamViews-method",
        "bamFiles<-,VariantFilteringResults-method",
        "browseVariants",
        "change",
        "change<-",
        "change<-,CutoffsList",
        "change<-,CutoffsList,ANY,character-method",
        "change<-,CutoffsList,ANY,integer-method",
        "change<-,CutoffsList,ANY,logical-method",
        "change<-,CutoffsList,ANY,numeric-method",
        "class:CutoffsList",
        "class:VariantFilteringResults",
        "cutoffs",
        "cutoffs,VariantFilteringResults-method",
        "cutoffs<-",
        "cutoffs<-,VariantFilteringResults,CutoffsList-method",
        "cutoffs<-,VariantFilteringResults,logical-method",
        "cutoffs<-,VariantFilteringResults-method",
        "CutoffsList",
        "CutoffsList-class",
        "filteredVariants",
        "filteredVariants,VariantFilteringResults-method",
        "filters",
        "filters,VariantFilteringResults-method",
        "filters<-",
        "filters<-,VariantFilteringResults-method",
        "filtersMetadata",
        "filtersMetadata,VariantFilteringParam-method",
        "filtersMetadata,VariantFilteringResults-method",
        "inheritanceModel",
        "inheritanceModel,VariantFilteringResults-method",
        "length",
        "length,VariantFilteringResults-method",
        "param",
        "param,VariantFilteringResults-method",
        "plot,VariantFilteringResults,ANY-method",
        "referenceGenome,VariantFilteringResults-method",
        "reportVariants",
        "reportVariants,VariantFilteringResults-method",
        "resetSamples",
        "resetSamples,VariantFilteringResults-method",
        "samples",
        "samples,VariantFilteringResults-method",
        "samples<-",
        "samples<-,VariantFilteringResults,character-method",
        "samples<-,VariantFilteringResults-method",
        "show,CompressedVRangesList-method",
        "show,VariantFilteringResults-method",
        "show,VariantFilteringResultsUI-method",
        "softFilterMatrix,VariantFilteringResults-method",
        "softFilterMatrix<-,VariantFilteringResults-method",
        "sog",
        "sog,VariantFilteringResults-method",
        "sortings",
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        "sortings<-",
        "sortings<-,VariantFilteringResults,CutoffsList-method",
        "summary,VariantFilteringResults-method",
        "VariantFilteringResults",
        "VariantFilteringResults-class"
      ]
    },
    {
      "page": "VariantType-class",
      "title": "FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType",
      "topics": [
        "downstream",
        "downstream,FiveSpliceSiteVariants-method",
        "downstream,ThreeSpliceSiteVariants-method",
        "downstream<-",
        "downstream<-,FiveSpliceSiteVariants-method",
        "downstream<-,ThreeSpliceSiteVariants-method",
        "FiveSpliceSiteVariants",
        "FiveSpliceSiteVariants-class",
        "minIntronLength",
        "minIntronLength,FiveSpliceSiteVariants-method",
        "minIntronLength,ThreeSpliceSiteVariants-method",
        "minIntronLength<-",
        "minIntronLength<-,FiveSpliceSiteVariants-method",
        "minIntronLength<-,ThreeSpliceSiteVariants-method",
        "show,FiveSpliceSiteVariants-method",
        "show,ThreeSpliceSiteVariants-method",
        "ThreeSpliceSiteVariants",
        "ThreeSpliceSiteVariants-class",
        "upstream",
        "upstream,FiveSpliceSiteVariants-method",
        "upstream,ThreeSpliceSiteVariants-method",
        "upstream<-",
        "upstream<-,FiveSpliceSiteVariants-method",
        "upstream<-,ThreeSpliceSiteVariants-method"
      ]
    },
    {
      "page": "WeightMatrix-class",
      "title": "Weight matrix class",
      "topics": [
        "conservedPositions",
        "conservedPositions,WeightMatrix-method",
        "readWm",
        "show,WeightMatrix-method",
        "WeightMatrix",
        "WeightMatrix-class",
        "width,WeightMatrix-method",
        "wmFilename",
        "wmFilename,WeightMatrix-method",
        "wmLocations",
        "wmLocations,WeightMatrix-method",
        "wmLocations<-",
        "wmLocations<-,WeightMatrix,character-method",
        "wmLocations<-,WeightMatrix-method",
        "wmName",
        "wmName,WeightMatrix-method",
        "wmScore",
        "wmScore,character,character-method",
        "wmScore,character,DNAStringSet-method",
        "wmScore,WeightMatrix,character-method",
        "wmScore,WeightMatrix,DNAStringSet-method",
        "wmStrictLocations",
        "wmStrictLocations,WeightMatrix-method",
        "wmStrictLocations<-",
        "wmStrictLocations<-,WeightMatrix,logical-method",
        "wmStrictLocations<-,WeightMatrix-method"
      ]
    },
    {
      "page": "xLinked",
      "title": "X-Linked inheritance analysis",
      "topics": [
        "xLinked",
        "xLinked,VariantFilteringParam-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/VariantFiltering/raw/RELEASE_3_23/README.md",
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