{
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  "Type": "Package",
  "Title": "Simulation of Tumor Clonal Evolution with Realistic Sequencing\nNoise",
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  "Authors@R": "c(\nperson(\"Gabriele\", \"Bucci\", email = \"bucci.g@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9838-7204\"))\n)",
  "Description": "ClonalSim generates realistic mutational profiles of tumor\nsamples with hierarchical clonal structure. It simulates\nfounder, shared, and private mutations with biologically\nrealistic noise models including intra-tumor heterogeneity\n(Beta distribution) and technical sequencing noise (negative\nbinomial depth variation, binomial read sampling, base errors).\nThe package is designed for benchmarking variant callers,\ntesting clonal deconvolution algorithms, and teaching tumor\nheterogeneity concepts.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "biocViews": "Software, Sequencing, SomaticMutation, VariantDetection,\nCoverage, Visualization, DataImport",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:07:19 UTC",
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  "Author": "Gabriele Bucci [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9838-7204>)",
  "Maintainer": "Gabriele Bucci <bucci.g@gmail.com>",
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      "page": "applyBiologicalNoise",
      "title": "Apply biological noise using Beta distribution",
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      "page": "ClonalSimData",
      "title": "Constructor for ClonalSimData",
      "topics": [
        "ClonalSimData"
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      "title": "ClonalSimData Class",
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        "ClonalSimData-class",
        "ClonalSimData-validity"
      ]
    },
    {
      "page": "getClonalStructure",
      "title": "Get clonal structure",
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      ]
    },
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      "title": "Get metadata",
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      ]
    },
    {
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      "title": "Get mutations data frame",
      "topics": [
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      ]
    },
    {
      "page": "getObservedVAF",
      "title": "Get observed VAF values (with sequencing noise)",
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      ]
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      "title": "Get true VAF values (biological, without sequencing noise)",
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      ]
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      "title": "Plot method for ClonalSimData",
      "topics": [
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      "page": "print.summary.ClonalSimData",
      "title": "Print summary method",
      "topics": [
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      "page": "show-ClonalSimData-method",
      "title": "Show method for ClonalSimData",
      "topics": [
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      ]
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    {
      "page": "simulateDepth",
      "title": "Simulate realistic sequencing depth",
      "topics": [
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      "topics": [
        "simulateSequencingReads"
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    {
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      "title": "Simulate tumor clonal evolution with realistic noise",
      "topics": [
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      "title": "Summary method for ClonalSimData",
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      "topics": [
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      "title": "Convert ClonalSimData to GRanges object",
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      "page": "toVCF",
      "title": "Convert ClonalSimData to VCF format",
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