{
  "_id": "6a2440a9a1338011a79f2018",
  "Package": "tidypq",
  "Title": "Tidyverse-Style Verbs for Phyloseq Objects",
  "Version": "0.1.0",
  "Authors@R": "person(\"Adrien\", \"Taudière\", , \"adrien.taudiere@zaclys.net\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1088-1182\"))",
  "Description": "Provides tidyverse-style verbs for manipulating phyloseq\nobjects at four scales: samples, taxa, occurrences, and tree.\nFunctions follow a consistent naming convention\n({verb}_{scale}_pq) and support data masking for intuitive\nfiltering, selection, and mutation operations.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/adrientaudiere/tidypq",
  "BugReports": "https://github.com/adrientaudiere/tidypq/issues",
  "Config/testthat/edition": "3",
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  "Config/pak/sysreqs": "libglpk-dev make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libxml2-dev xz-utils zlib1g-dev",
  "Repository": "https://adrientaudiere.r-universe.dev",
  "Date/Publication": "2026-03-13 13:36:55 UTC",
  "RemoteUrl": "https://github.com/adrientaudiere/tidypq",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
  },
  "Author": "Adrien Taudière [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1088-1182>)",
  "Maintainer": "Adrien Taudière <adrien.taudiere@zaclys.net>",
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      "package": "phyloseq",
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  "_selfowned": true,
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  "_stars": 1,
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
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    "manual.pdf"
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  "_cranurl": false,
  "_exports": [
    "arrange_samples_pq",
    "arrange_taxa_pq",
    "chimera_removal_dada2",
    "create_chimera_pq",
    "decontam_sam_control",
    "decontam_taxa_control",
    "filter_occurrences_pq",
    "filter_samples_pq",
    "filter_taxa_pq",
    "filter_tree_pq",
    "mutate_occurrences_pq",
    "mutate_samdata_pq",
    "mutate_taxa_pq",
    "plot_sample_depth_pq",
    "rename_samples_pq",
    "rename_taxa_pq",
    "select_samdata_pq",
    "select_taxa_pq",
    "slice_samples_pq",
    "slice_taxa_pq",
    "taxa_prevalence"
  ],
  "_help": [
    {
      "page": "arrange_samples_pq",
      "title": "Arrange samples by column values",
      "topics": [
        "arrange_samples_pq"
      ]
    },
    {
      "page": "arrange_taxa_pq",
      "title": "Arrange taxa by column values",
      "topics": [
        "arrange_taxa_pq"
      ]
    },
    {
      "page": "chimera_removal_dada2",
      "title": "Remove chimeric sequences using dada2",
      "topics": [
        "chimera_removal_dada2"
      ]
    },
    {
      "page": "create_chimera_pq",
      "title": "Create a phyloseq object with synthetic chimeric sequences",
      "topics": [
        "create_chimera_pq"
      ]
    },
    {
      "page": "decontam_sam_control",
      "title": "Decontaminate based on negative/blank control samples",
      "topics": [
        "decontam_sam_control"
      ]
    },
    {
      "page": "decontam_taxa_control",
      "title": "Decontaminate based on control taxa",
      "topics": [
        "decontam_taxa_control"
      ]
    },
    {
      "page": "filter_occurrences_pq",
      "title": "Filter occurrences in the OTU table",
      "topics": [
        "filter_occurrences_pq"
      ]
    },
    {
      "page": "filter_samples_pq",
      "title": "Filter samples in a phyloseq object",
      "topics": [
        "filter_samples_pq"
      ]
    },
    {
      "page": "filter_taxa_pq",
      "title": "Filter taxa in a phyloseq object",
      "topics": [
        "filter_taxa_pq"
      ]
    },
    {
      "page": "filter_tree_pq",
      "title": "Filter phyloseq by tree topology",
      "topics": [
        "filter_tree_pq"
      ]
    },
    {
      "page": "mutate_occurrences_pq",
      "title": "Transform OTU table values",
      "topics": [
        "mutate_occurrences_pq"
      ]
    },
    {
      "page": "mutate_samdata_pq",
      "title": "Add or modify columns in sample_data",
      "topics": [
        "mutate_samdata_pq"
      ]
    },
    {
      "page": "mutate_taxa_pq",
      "title": "Add or modify columns in tax_table",
      "topics": [
        "mutate_taxa_pq"
      ]
    },
    {
      "page": "plot_sample_depth_pq",
      "title": "Plot sample depth differences to detect outliers",
      "topics": [
        "plot_sample_depth_pq"
      ]
    },
    {
      "page": "rename_samples_pq",
      "title": "Rename columns in sample_data",
      "topics": [
        "rename_samples_pq"
      ]
    },
    {
      "page": "rename_taxa_pq",
      "title": "Rename columns in tax_table",
      "topics": [
        "rename_taxa_pq"
      ]
    },
    {
      "page": "select_samdata_pq",
      "title": "Select columns from sample_data in a phyloseq object",
      "topics": [
        "select_samdata_pq"
      ]
    },
    {
      "page": "select_taxa_pq",
      "title": "Select columns from tax_table in a phyloseq object",
      "topics": [
        "select_taxa_pq"
      ]
    },
    {
      "page": "slice_samples_pq",
      "title": "Subset samples by position",
      "topics": [
        "slice_samples_pq"
      ]
    },
    {
      "page": "slice_taxa_pq",
      "title": "Subset taxa by position",
      "topics": [
        "slice_taxa_pq"
      ]
    },
    {
      "page": "taxa_prevalence",
      "title": "Calculate taxa prevalence",
      "topics": [
        "taxa_prevalence"
      ]
    }
  ],
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