{
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  "Package": "jellyfisher",
  "Title": "Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots",
  "Version": "1.1.1",
  "Authors@R": "person(\"Kari\", \"Lavikka\", , \"kari.lavikka@helsinki.fi\", role = c(\"cph\", \"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4163-4945\"))",
  "Description": "Generates interactive Jellyfish plots to visualize\nspatiotemporal tumor evolution by integrating sample and\nphylogenetic trees into a unified plot. This approach provides\nan intuitive way to analyze tumor heterogeneity and evolution\nover time and across anatomical locations. The Jellyfish plot\nvisualization design was first introduced by Lahtinen, Lavikka,\net al. (2023, <doi:10.1016/j.ccell.2023.04.017>). This package\nalso supports visualizing ClonEvol results, a tool developed by\nDang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing\nclonal evolution from multi-sample sequencing data. The\n'clonevol' package is not available on CRAN but can be\ninstalled from its GitHub repository\n(<https://github.com/hdng/clonevol>).",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "URL": "https://github.com/HautaniemiLab/jellyfisher,\nhttps://hautaniemilab.github.io/jellyfisher/",
  "BugReports": "https://github.com/HautaniemiLab/jellyfisher/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "Visualization, Phylogenetics, Software, Spatial",
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  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://hautaniemilab.r-universe.dev",
  "Date/Publication": "2025-11-26 12:35:24 UTC",
  "RemoteUrl": "https://github.com/hautaniemilab/jellyfisher",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 07:54:27 UTC",
    "User": "root"
  },
  "Author": "Kari Lavikka [cph, aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4163-4945>)",
  "Maintainer": "Kari Lavikka <kari.lavikka@helsinki.fi>",
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    "author": "Kari Lavikka <kari.lavikka@helsinki.fi>",
    "committer": "Kari Lavikka <kari.lavikka@helsinki.fi>",
    "message": "docs: add proper CITATION file\n",
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    "email": "kari.lavikka@helsinki.fi",
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    "description": "PhD, visualization of cancer genomes and tumor evolution",
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      "date": "2025-11-25"
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    "phylogenetics",
    "software",
    "spatial",
    "bioinformatics",
    "phylogenetic-analysis",
    "tumor-evolution",
    "tumor-heterogeneity",
    "visualization-tool"
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    "name": "Hautaniemi Lab",
    "description": "The Systems Biology of Drug Resistance in Cancer group, University of Helsinki"
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    "extract_tables_from_clonevol",
    "jellyfisher",
    "jellyfisherOutput",
    "renderJellyfisher",
    "select_patients",
    "set_parents",
    "set_ranks"
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      "title": "Jellyfisher example data",
      "object": "jellyfisher_example_tables",
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      ],
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      "page": "add_inferred_sample",
      "title": "Insert an a hypothetical inferred sample into the sample tree and set it as the parent of specified samples.",
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      ]
    },
    {
      "page": "extract_tables_from_clonevol",
      "title": "Extract Data for Jellyfisher from ClonEvol Results",
      "topics": [
        "extract_tables_from_clonevol"
      ]
    },
    {
      "page": "jellyfisher",
      "title": "Creates a Jellyfish plot",
      "topics": [
        "jellyfisher"
      ]
    },
    {
      "page": "jellyfisher_example_tables",
      "title": "Jellyfisher example data",
      "topics": [
        "jellyfisher_example_tables"
      ]
    },
    {
      "page": "jellyfisher-shiny",
      "title": "Shiny bindings for jellyfisher",
      "topics": [
        "jellyfisher-shiny",
        "jellyfisherOutput",
        "renderJellyfisher"
      ]
    },
    {
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      "title": "Filter Jellyfish tables by patient",
      "topics": [
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      ]
    },
    {
      "page": "set_parents",
      "title": "Set parents for samples",
      "topics": [
        "set_parents"
      ]
    },
    {
      "page": "set_ranks",
      "title": "Set ranks for samples",
      "topics": [
        "set_ranks"
      ]
    },
    {
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      "title": "Validate Jellyfish tables",
      "topics": [
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      ]
    }
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        "Plotting with custom options",
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      "created": "2025-02-05 10:24:00",
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