{
  "_id": "6aacfc133d719c1f840741f7",
  "Package": "hidecan",
  "Title": "Create HIDECAN Plots for Visualising Genome-Wide Association\nStudies and Differential Expression Results",
  "Version": "1.2.0.0",
  "Authors@R": "person(\"Olivia\", \"Angelin-Bonnet\", , \"olivia.angelin-bonnet@plantandfood.co.nz\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7708-2919\"))",
  "Description": "Generates HIDECAN plots that summarise and combine the\nresults of QTL mapping, genome-wide association studies (GWAS)\nand transcriptomics differential expression analyses (DE),\nalong with manually curated candidate genes of interest. The\nHIDECAN plot is presented in Angelin-Bonnet, O., Vignes, M.,\nBiggs, P. J., Baldwin, S., & Thomson, S. (2024). Visual\nIntegration of Genome-Wide Association Studies and Differential\nExpression Results with the Hidecan R Package. Genes, 15(10),\n1244.",
  "License": "MIT + file LICENSE",
  "URL": "https://plantandfoodresearch.github.io/hidecan/,\nhttps://github.com/PlantandFoodResearch/hidecan",
  "BugReports": "https://github.com/PlantandFoodResearch/hidecan/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Language": "en-GB",
  "Repository": "https://plantandfoodresearch.r-universe.dev",
  "Date/Publication": "2025-07-17 02:33:44 UTC",
  "RemoteUrl": "https://github.com/plantandfoodresearch/hidecan",
  "RemoteRef": "HEAD",
  "RemoteSha": "bba89676b4d2d71dd2259156a8fe4314dbb7ca47",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-18 08:16:50 UTC",
    "User": "root"
  },
  "Author": "Olivia Angelin-Bonnet [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7708-2919>)",
  "Maintainer": "Olivia Angelin-Bonnet <olivia.angelin-bonnet@plantandfood.co.nz>",
  "_user": "plantandfoodresearch",
  "_type": "src",
  "_file": "hidecan_1.2.0.0.tar.gz",
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  "_expires": "2026-12-27T08:53:36.000Z",
  "_created": "2026-09-18T08:16:50.000Z",
  "_published": "2026-09-18T08:53:39.135Z",
  "_jobs": [
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  "_upstream": "https://github.com/plantandfoodresearch/hidecan",
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    "author": "Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>",
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    "message": "Merge pull request #16 from oliviaAB/adding-qtl\n\nFixed missing QTL point shape",
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    "name": "Olivia Angelin-Bonnet",
    "email": "olivia.angelin-bonnet@plantandfood.co.nz",
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  "_selfowned": true,
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  "_updates": [],
  "_tags": [],
  "_stars": 8,
  "_contributors": [
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    "name": "Plant and Food Research",
    "followers": 96,
    "description": "The New Zealand Institute for Plant and Food Research. Crown Research Institute. Contact Matthew Laurenson or Zane Gilmore for access."
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hidecan"
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  "_pkgdown": "https://plantandfoodresearch.github.io/hidecan/",
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hidecan.html",
    "extra/manual.pdf",
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    "extra/readme.md",
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  "_cranurl": true,
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      "date": "2023-02-10"
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  "_exports": [
    ".compute_chrom_length_genes",
    ".compute_chrom_length_markers",
    "apply_threshold",
    "CAN_data",
    "combine_chrom_length",
    "compute_chrom_length",
    "create_hidecan_plot",
    "CUSTOM_data",
    "DE_data",
    "get_example_data",
    "GWAS_data",
    "GWAS_data_from_gwaspoly",
    "hidecan_aes",
    "hidecan_plot",
    "hidecan_plot_from_gwaspoly",
    "manhattan_plot",
    "QTL_data",
    "run_hidecan_shiny"
  ],
  "_help": [
    {
      "page": "dot-add_data_type",
      "title": "Add data type to HIDECAN plot",
      "topics": [
        ".add_data_type"
      ]
    },
    {
      "page": "dot-check_chrom_limits",
      "title": "Check chromosome limits",
      "topics": [
        ".check_chrom_limits"
      ]
    },
    {
      "page": "dot-check_chroms",
      "title": "Check chromosomes to plot",
      "topics": [
        ".check_chroms"
      ]
    },
    {
      "page": "dot-check_cols",
      "title": "Checks whether some columns are present in a tibble",
      "topics": [
        ".check_cols"
      ]
    },
    {
      "page": "dot-compute_chrom_length_genes",
      "title": "Computes chromosomes' length for a tibble of genes",
      "topics": [
        ".compute_chrom_length_genes"
      ]
    },
    {
      "page": "dot-compute_chrom_length_markers",
      "title": "Computes chromosomes' length for a tibble of markers",
      "topics": [
        ".compute_chrom_length_markers"
      ]
    },
    {
      "page": "dot-get_aes_type",
      "title": "Returns either \"aes_type\" attribute or object class",
      "topics": [
        ".get_aes_type"
      ]
    },
    {
      "page": "dot-get_plot_aes",
      "title": "Computes plot aesthetics",
      "topics": [
        ".get_plot_aes"
      ]
    },
    {
      "page": "apply_threshold",
      "title": "Filters GWAS, DE or QTL mapping results based on a threshold",
      "topics": [
        "apply_threshold",
        "apply_threshold.CAN_data",
        "apply_threshold.CUSTOM_data",
        "apply_threshold.default",
        "apply_threshold.DE_data",
        "apply_threshold.GWAS_data",
        "apply_threshold.QTL_data"
      ]
    },
    {
      "page": "CAN_data",
      "title": "Creates a 'CAN_data' object",
      "topics": [
        "CAN_data"
      ]
    },
    {
      "page": "combine_chrom_length",
      "title": "Computes chromosomes' length from list",
      "topics": [
        "combine_chrom_length"
      ]
    },
    {
      "page": "compute_chrom_length",
      "title": "Computes chromosomes' length",
      "topics": [
        "compute_chrom_length",
        "compute_chrom_length.CAN_data",
        "compute_chrom_length.CUSTOM_data",
        "compute_chrom_length.DE_data",
        "compute_chrom_length.GWAS_data",
        "compute_chrom_length.QTL_data"
      ]
    },
    {
      "page": "create_hidecan_plot",
      "title": "Creates a HIDECAN plot",
      "topics": [
        "create_hidecan_plot"
      ]
    },
    {
      "page": "CUSTOM_data",
      "title": "Creates a 'CUSTOM_data' object",
      "topics": [
        "CUSTOM_data"
      ]
    },
    {
      "page": "DE_data",
      "title": "Creates a 'DE_data' object",
      "topics": [
        "DE_data"
      ]
    },
    {
      "page": "get_example_data",
      "title": "Example dataset",
      "topics": [
        "get_example_data"
      ]
    },
    {
      "page": "GWAS_data",
      "title": "Creates a 'GWAS_data' object",
      "topics": [
        "GWAS_data"
      ]
    },
    {
      "page": "GWAS_data_from_gwaspoly",
      "title": "Extracts information from GWASpoly output",
      "topics": [
        "GWAS_data_from_gwaspoly"
      ]
    },
    {
      "page": "hidecan_aes",
      "title": "Default aesthetics for HIDECAN plot",
      "topics": [
        "hidecan_aes"
      ]
    },
    {
      "page": "hidecan_plot",
      "title": "Wrapper to create a HIDECAN plot",
      "topics": [
        "hidecan_plot"
      ]
    },
    {
      "page": "hidecan_plot_from_gwaspoly",
      "title": "Creates a HIDECAN plot from GWASpoly output",
      "topics": [
        "hidecan_plot_from_gwaspoly"
      ]
    },
    {
      "page": "manhattan_plot",
      "title": "Creates a Manhattan plot",
      "topics": [
        "manhattan_plot"
      ]
    },
    {
      "page": "new_CAN_data",
      "title": "'CAN_data' constructor",
      "topics": [
        "new_CAN_data"
      ]
    },
    {
      "page": "new_CUSTOM_data",
      "title": "'CUSTOM_data' constructor",
      "topics": [
        "new_CUSTOM_data"
      ]
    },
    {
      "page": "new_DE_data",
      "title": "'DE_data' constructor",
      "topics": [
        "new_DE_data"
      ]
    },
    {
      "page": "new_GWAS_data",
      "title": "'GWAS_data' constructor",
      "topics": [
        "new_GWAS_data"
      ]
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      "page": "new_QTL_data",
      "title": "'QTL_data' constructor",
      "topics": [
        "new_QTL_data"
      ]
    },
    {
      "page": "QTL_data",
      "title": "Creates a 'QTL_data' object",
      "topics": [
        "QTL_data"
      ]
    },
    {
      "page": "run_hidecan_shiny",
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      "topics": [
        "run_hidecan_shiny"
      ]
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      "topics": [
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        "validate_DE_data"
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      "topics": [
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      "title": "Checks validity of input for 'QTL_data' constructor",
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        "Input data",
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        "Selecting chromosomes and genomic positions",
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}