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  "Package": "molpathR",
  "Title": "Molecular Pathology Data Platform for Clinical NGS Integration",
  "Description": "A unified platform for ingesting, linking, querying, and\nvisualizing molecular pathology data from heterogeneous sources\nincluding NGS files (FASTQ, BAM, VCF), XML variant\ninterpretation reports, structured pathology PDF reports,\npathology and clinical information systems, and survival\noutcome data. Provides a searchable in-memory database and an\ninteractive Shiny application for clinical exploration and\ncohort analysis. Raw sequence and alignment readers do not\nperform variant calling or clinical interpretation.",
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  "Repository": "https://cttir.r-universe.dev",
  "Date/Publication": "2026-11-03 11:54:04 UTC",
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    {
      "page": "mp_build_db",
      "title": "Build a molpath_db from parsed data objects",
      "topics": [
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    {
      "page": "mp_example_db",
      "title": "Create a synthetic molecular pathology database",
      "topics": [
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    },
    {
      "page": "mp_example_files",
      "title": "Write synthetic example files to a directory",
      "topics": [
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    },
    {
      "page": "mp_get_patient",
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      "topics": [
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    },
    {
      "page": "mp_load_db",
      "title": "Load a molpath_db from disk",
      "topics": [
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    },
    {
      "page": "mp_merge_db",
      "title": "Merge two molpath_db objects",
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      "page": "mp_plot_cohort_overview",
      "title": "Plot cohort overview",
      "topics": [
        "mp_plot_cohort_overview"
      ]
    },
    {
      "page": "mp_plot_mutation_spectrum",
      "title": "Plot mutation spectrum",
      "topics": [
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    },
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      "page": "mp_plot_survival",
      "title": "Plot Kaplan-Meier survival curves",
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    },
    {
      "page": "mp_plot_timeline",
      "title": "Plot patient timeline",
      "topics": [
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    },
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      "page": "mp_plot_vaf_distribution",
      "title": "Plot variant allele frequency distribution",
      "topics": [
        "mp_plot_vaf_distribution"
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    },
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      "page": "mp_plot_variant_landscape",
      "title": "Plot variant landscape (oncoplot)",
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      "page": "mp_query_patients",
      "title": "Filter patients in a molpath_db",
      "topics": [
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    },
    {
      "page": "mp_query_samples",
      "title": "Filter samples in a molpath_db",
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    },
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      "page": "mp_query_variants",
      "title": "Filter variants in a molpath_db",
      "topics": [
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    {
      "page": "mp_read_auto",
      "title": "Automatically read a molecular pathology file",
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      "title": "Read a BAM file",
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    {
      "page": "mp_read_fastq",
      "title": "Read a FASTQ file",
      "topics": [
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    {
      "page": "mp_read_nexus_clinical",
      "title": "Read Nexus clinical data",
      "topics": [
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    {
      "page": "mp_read_nexus_pathology",
      "title": "Read Nexus pathology data",
      "topics": [
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      "title": "Read an XML variant report",
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      "title": "Cohort-level summary of a molpath_db",
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