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  "Title": "Simulation, Visualization and Comparison of Tumor Evolution Data",
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  "Description": "Simulating, visualizing and comparing tumor clonal data by\nusing simple commands. This aims at providing a tool to help\nresearchers to easily simulate tumor data and analyze the\nresults of their approaches for studying the composition and\nthe evolutionary history of tumors.",
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  "Author": "Aitor Sánchez-Ferrera [cre, aut] (ORCID:\n<https://orcid.org/0000-0001-6127-0686>), Maitena\nTellaetxe-Abete [aut] (ORCID:\n<https://orcid.org/0000-0003-1894-4547>), Borja Calvo [aut]\n(ORCID: <https://orcid.org/0000-0001-9969-9664>)",
  "Maintainer": "Aitor Sánchez-Ferrera <aitor.sanchezf@ehu.eus>",
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  "Date/Publication": "2025-11-12 13:40:02 UTC",
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      "title": "A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika'",
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      "page": "add_noise",
      "title": "Add noise to the VAF values in an F matrix",
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    {
      "page": "B_mats",
      "title": "A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika'",
      "topics": [
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      ]
    },
    {
      "page": "B_to_phylotree",
      "title": "Create a 'Phylotree' object from a 'B' matrix.",
      "topics": [
        "B_to_phylotree"
      ]
    },
    {
      "page": "combine_trees",
      "title": "Get consensus tree between two phylogenetic trees",
      "topics": [
        "combine_trees"
      ]
    },
    {
      "page": "create_B",
      "title": "Create tumor phylogenetic tree topology",
      "topics": [
        "create_B"
      ]
    },
    {
      "page": "create_F",
      "title": "Calculate the variant allele frequency (VAF) values in a set of samples",
      "topics": [
        "create_F"
      ]
    },
    {
      "page": "create_instance",
      "title": "Create a tumor phylogenetic tree instance",
      "topics": [
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      ]
    },
    {
      "page": "create_phylotree",
      "title": "Create a 'Phylotree' object",
      "topics": [
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      ]
    },
    {
      "page": "create_U",
      "title": "Calculate tumor clone frequencies in samples",
      "topics": [
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      ]
    },
    {
      "page": "equals",
      "title": "Check if two phylogenetic trees are equal",
      "topics": [
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      ]
    },
    {
      "page": "find_common_subtrees",
      "title": "Find the set of common subtrees between two phylogenetic trees",
      "topics": [
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      ]
    },
    {
      "page": "palettes",
      "title": "Palettes for the methods of 'GeRnika'",
      "topics": [
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    },
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      "title": "S4 class to represent phylogenetic trees.",
      "topics": [
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      ]
    },
    {
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      "title": "Plot a Phylotree object.",
      "topics": [
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        "plot,Phylotree-method"
      ]
    },
    {
      "page": "plot_proportions",
      "title": "Plot a phylogenetic tree with proportional node sizes and colors",
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      ]
    }
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      "source": "models.Rmd",
      "filename": "models.html",
      "title": "Simulation of tumor clonal data (advanced users)",
      "author": "Aitor Sánchez, Maitena Tellaetxe and Borja Calvo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview of the data instances",
        "Overview of the data parameters",
        "Basic instantiation",
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        "Digging into the models",
        "Tumor model",
        "Sampling model",
        "Sequencing noise model",
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      "title": "Usage of GeRnika",
      "author": "Aitor Sánchez, Maitena Tellaetxe and Borja Calvo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Simulating tumor clonal data",
        "Topology parameter k",
        "Simulate a tumor with k=0:",
        "Simulate a tumor with k=1:",
        "Create a Phylotree class object for each tumor:",
        "Plot both trees",
        "Sequencing noise",
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        "Instantiation of Phylotree class objects",
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