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  "Package": "mclink",
  "Title": "Metabolic Pathway Completeness and Abundance Calculation",
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  "Description": "Provides tools for analyzing metabolic pathway\ncompleteness, abundance, and transcripts using KEGG Orthology\n(KO) data from (meta)genomic and (meta)transcriptomic studies.\nSupports both completeness (presence/absence) and\nabundance-weighted analyses. Includes built-in KEGG reference\ndatasets. For more details see Li et al. (2023)\n<doi:10.1038/s41467-023-42193-7>.",
  "URL": "https://github.com/LiuyangLee/mclink",
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  "Author": "Liuyang Li [aut, cre] (<https://orcid.org/0000-0001-6004-9437>)",
  "Maintainer": "Liuyang Li <cyanobacteria@yeah.net>",
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    "process_step_space",
    "read_and_process_KO_table",
    "read_and_process_pathway_infor",
    "remove_outer_brackets"
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      "file": "KO_pathway_ref.rda",
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        "Module_Type",
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        "Level_3",
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      "title": "KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes",
      "object": "KO_Sample_wide",
      "file": "KO_Sample_wide.rda",
      "class": [
        "data.frame"
      ],
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        "Marinobacter salarius",
        "Pseudooceanicola nanhaiensis",
        "Alteromonas australica",
        "Henriciella pelagia"
      ],
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      "table": true,
      "tojson": true
    }
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      "page": "add_rows_if_not_exists",
      "title": "Add Missing Rows to a Data Frame",
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    },
    {
      "page": "ata_cal",
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      "title": "Convert Abundance Values to Presence/Absence Indicators",
      "topics": [
        "convert_abundance_to_presence"
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      "page": "create_sub_module_sample",
      "title": "Create and Export Pathway-Specific Module Sample Files",
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    {
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      "title": "Escape Special Characters in a String",
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    },
    {
      "page": "extract_inner_brackets",
      "title": "Extract Innermost Parentheses Content",
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    },
    {
      "page": "group_ko_by_module",
      "title": "Group KO Abundance Data by Module",
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      "topics": [
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      "topics": [
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    {
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      "title": "Metabolic Pathway Coverage Analysis",
      "topics": [
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    },
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      "topics": [
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    },
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