{
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  "Package": "mclink",
  "Title": "Metabolic Pathway Completeness and Abundance Calculation",
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  "Authors@R": "person(given = \"Liuyang\",\nfamily = \"Li\",\nemail = \"cyanobacteria@yeah.net\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6004-9437\"))",
  "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",
  "BugReports": "https://github.com/LiuyangLee/mclink/issues",
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  "Encoding": "UTF-8",
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    "User": "root"
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  "Author": "Liuyang Li [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6004-9437>)",
  "Maintainer": "Liuyang Li <cyanobacteria@yeah.net>",
  "Repository": "https://cran.r-universe.dev",
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    "add_rows_if_not_exists",
    "ata_cal",
    "convert_abundance_to_presence",
    "create_sub_module_sample",
    "escape_special_chars",
    "extract_inner_brackets",
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    "merge_module_name",
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    "process_module_brackets",
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    "process_module_loop_plus",
    "process_module_step",
    "process_module_structure",
    "process_step_comma",
    "process_step_direct",
    "process_step_plus",
    "process_step_space",
    "read_and_process_KO_table",
    "read_and_process_pathway_infor",
    "remove_outer_brackets"
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      "name": "KO_pathway_ref",
      "title": "KEGG Orthology (KO) Pathway Information Dataset",
      "object": "KO_pathway_ref",
      "file": "KO_pathway_ref.rda",
      "class": [
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      ],
      "fields": [
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        "Module_Type",
        "Level_2",
        "Level_3",
        "Module_Entry",
        "Module_Name",
        "Definition",
        "Orthology_Symbol",
        "Orthology_Name",
        "KO_Symbol"
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      "tojson": true
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    {
      "name": "KO_Sample_wide",
      "title": "KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes",
      "object": "KO_Sample_wide",
      "file": "KO_Sample_wide.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "KO",
        "Marinobacter salarius",
        "Pseudooceanicola nanhaiensis",
        "Alteromonas australica",
        "Henriciella pelagia"
      ],
      "rows": 2495,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_rows_if_not_exists",
      "title": "Add Missing Rows to a Data Frame",
      "topics": [
        "add_rows_if_not_exists"
      ]
    },
    {
      "page": "ata_cal",
      "title": "Calculate Log2 Ratio of Sample Values to Row Means",
      "topics": [
        "ata_cal"
      ]
    },
    {
      "page": "convert_abundance_to_presence",
      "title": "Convert Abundance Values to Presence/Absence Indicators",
      "topics": [
        "convert_abundance_to_presence"
      ]
    },
    {
      "page": "create_sub_module_sample",
      "title": "Create and Export Pathway-Specific Module Sample Files",
      "topics": [
        "create_sub_module_sample"
      ]
    },
    {
      "page": "escape_special_chars",
      "title": "Escape Special Characters in a String",
      "topics": [
        "escape_special_chars"
      ]
    },
    {
      "page": "extract_inner_brackets",
      "title": "Extract Innermost Parentheses Content",
      "topics": [
        "extract_inner_brackets"
      ]
    },
    {
      "page": "group_ko_by_module",
      "title": "Group KO Abundance Data by Module",
      "topics": [
        "group_ko_by_module"
      ]
    },
    {
      "page": "KO_pathway_ref",
      "title": "KEGG Orthology (KO) Pathway Information Dataset",
      "topics": [
        "KO_pathway_ref"
      ]
    },
    {
      "page": "KO_Sample_wide",
      "title": "KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes",
      "topics": [
        "KO_Sample_wide"
      ]
    },
    {
      "page": "mclink",
      "title": "Metabolic Pathway Coverage Analysis",
      "topics": [
        "mclink"
      ]
    },
    {
      "page": "merge_module_name",
      "title": "Merge Module Information with Module Table",
      "topics": [
        "merge_module_name"
      ]
    },
    {
      "page": "process_all_modules",
      "title": "Process All Modules in Pathway Information",
      "topics": [
        "process_all_modules"
      ]
    },
    {
      "page": "process_all_pathways",
      "title": "Process All Pathways Analysis",
      "topics": [
        "process_all_pathways"
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    },
    {
      "page": "process_module_brackets",
      "title": "Process Module Brackets Recursively",
      "topics": [
        "process_module_brackets"
      ]
    },
    {
      "page": "process_module_definition",
      "title": "Process Module Definition String",
      "topics": [
        "process_module_definition"
      ]
    },
    {
      "page": "process_module_loop_comma",
      "title": "Process Module Components with Comma Handling",
      "topics": [
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      ]
    },
    {
      "page": "process_module_loop_plu_comma",
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      "topics": [
        "process_module_loop_plu_comma"
      ]
    },
    {
      "page": "process_module_loop_plus",
      "title": "Process Module Components with Plus Sign Handling",
      "topics": [
        "process_module_loop_plus"
      ]
    },
    {
      "page": "process_module_step",
      "title": "Process Module Steps with Complex KO String Handling",
      "topics": [
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      ]
    },
    {
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      "title": "Process Module Structure Data",
      "topics": [
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      "topics": [
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      "topics": [
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      "topics": [
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    },
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      "title": "Remove Outer Parentheses from String",
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