{
  "_id": "6a1969ecacfb0bcc41de95f9",
  "Package": "cageminer",
  "Title": "Candidate Gene Miner",
  "Version": "1.19.0",
  "Authors@R": "c(\nperson(given = \"Fabrício\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\")),\nperson(given = \"Thiago\",\nfamily = \"Venancio\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-2215-8082\"))\n)",
  "Description": "This package aims to integrate GWAS-derived SNPs and\ncoexpression networks to mine candidate genes associated with a\nparticular phenotype. For that, users must define a set of\nguide genes, which are known genes involved in the studied\nphenotype. Additionally, the mined candidates can be given a\nscore that favor candidates that are hubs and/or transcription\nfactors. The scores can then be used to rank and select the top\nn most promising genes for downstream experiments.",
  "License": "GPL-3",
  "URL": "https://github.com/almeidasilvaf/cageminer",
  "BugReports": "https://support.bioconductor.org/t/cageminer",
  "biocViews": "Software, SNP, FunctionalPrediction, GenomeWideAssociation,\nGeneExpression, NetworkEnrichment, VariantAnnotation,\nFunctionalGenomics, Network",
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  "Config/testthat/edition": "3",
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  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev perl xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:32 UTC",
  "RemoteUrl": "https://github.com/bioc/cageminer",
  "RemoteRef": "HEAD",
  "RemoteSha": "2cc1c547e19b48f96e14f4870500cbf64c5a4a55",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:35:08 UTC",
    "User": "root"
  },
  "Author": "Fabrício Almeida-Silva [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5314-2964>),\nThiago Venancio [aut] (ORCID: <https://orcid.org/0000-0002-2215-8082>)",
  "Maintainer": "Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>",
  "MD5sum": "84374f811b36c00a96c7bbb29fc191f4",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-29T08:35:08.000Z",
  "_published": "2026-05-29T10:26:52.136Z",
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    "description": "Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.",
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      "title": "Pepper chromosome lengths",
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      "file": "chr_length.rda",
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      ],
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        "Module",
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      ],
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        "cor",
        "pvalue"
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      "class": [
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      "table": false,
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      "class": [
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        "Family"
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      "table": true,
      "tojson": true
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      "page": "chr_length",
      "title": "Pepper chromosome lengths",
      "topics": [
        "chr_length"
      ]
    },
    {
      "page": "gcn",
      "title": "Simulation of the output list from BioNERO::exp2gcn() with pepper data",
      "topics": [
        "gcn"
      ]
    },
    {
      "page": "gene_ranges",
      "title": "Genomic coordinates of pepper genes",
      "topics": [
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      ]
    },
    {
      "page": "guides",
      "title": "Guide genes associated with defense and resistance to oomycetes",
      "topics": [
        "guides"
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    },
    {
      "page": "hubs",
      "title": "Example hub genes for the network stored in the gcn object",
      "topics": [
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    {
      "page": "mine_candidates",
      "title": "Mine high-confidence candidate genes in a single step",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Step 3: Select candidates based on gene significance",
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      "title": "Example output from mine_step2()",
      "topics": [
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      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Score candidate genes and select the top n genes",
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      "title": "Pepper transcription factors",
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