{
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  "Package": "Paralogs",
  "Type": "Package",
  "Title": "Visualizing Differential Expression of Paralogs in KEGG Gene\nPathways",
  "Version": "0.2.1",
  "Authors@R": "person(\"Carson\", \"Stacy\", email = \"clstacy.stat@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "This package provides functions to visualize the\ndifferential expression of paralogs in KEGG gene pathways. The\npackage includes functions to download KEGG gene pathways,\nextract paralogs from the pathways, and visualize the\ndifferential expression of the paralogs. The package also\nincludes functions to visualize the expression of paralogs in\nthe context of the KEGG gene pathways.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "suggests": "org.Sc.sgd.db, clusterProfiler",
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  "Repository": "https://clstacy.r-universe.dev",
  "Date/Publication": "2025-03-13 14:51:24 UTC",
  "RemoteUrl": "https://github.com/clstacy/Paralogs",
  "RemoteRef": "HEAD",
  "RemoteSha": "7c1ba2bfc174fbd433511c07a1cb1387a9952827",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 09:25:35 UTC",
    "User": "root"
  },
  "Author": "Carson Stacy [aut, cre]",
  "Maintainer": "Carson Stacy <clstacy.stat@gmail.com>",
  "MD5sum": "fd7755cf94e4f0e857922c70cad47d42",
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  "_published": "2026-05-29T11:05:29.864Z",
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    "author": "Carson Stacy <clstacy@uark.edu>",
    "committer": "Carson Stacy <clstacy@uark.edu>",
    "message": "Remove duplicated plotting function, fix spacing bug\n",
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    "email": "clstacy.stat@gmail.com",
    "login": "clstacy",
    "twitter": "@carsonlstacy",
    "description": "Molecular Cell Biology and Statistics. University of Arkansas",
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      "package": "dplyr",
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      "package": "KEGGREST",
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  "_exports": [
    "%>%",
    "create_ggkegg",
    "createParalogPlots",
    "fetchKeggReactions",
    "getPathwayNumber",
    "loadEnrichResults",
    "loadGeneData",
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    {
      "name": "example_enrich_results",
      "title": "An example output of enrichKEGG is provided in the 'example_enrich_results' dataset. The results are the top enrichments for the genes in the lrt_yeast example. This data is used in vignette examples.",
      "object": "example_enrich_results",
      "class": [
        "enrichResult"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "lrt_yeast",
      "title": "An example DGELRT object is provided in the 'lrt_yeast' dataset. This object contains the results of a differential gene expression analysis using the edgeR package. logFC values correspond to the effect of a gene knockout on response to ethanol stress in yeast.",
      "object": "lrt_yeast",
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      "tojson": false
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    {
      "page": "create_ggkegg",
      "title": "Create ggkegg Object for KEGG Pathway Visualization",
      "topics": [
        "create_ggkegg"
      ]
    },
    {
      "page": "createParalogPlots",
      "title": "Create KEGG Pathway Graphs",
      "topics": [
        "createParalogPlots"
      ]
    },
    {
      "page": "example_enrich_results",
      "title": "An example output of enrichKEGG is provided in the `example_enrich_results` dataset. The results are the top enrichments for the genes in the lrt_yeast example. This data is used in vignette examples.",
      "topics": [
        "example_enrich_results"
      ]
    },
    {
      "page": "fetchKeggReactions",
      "title": "Fetch KEGG Reactions",
      "topics": [
        "fetchKeggReactions"
      ]
    },
    {
      "page": "getPathwayNumber",
      "title": "Get Pathway Number to match row of enrichKEGG to KEGG pathway of interest",
      "topics": [
        "getPathwayNumber"
      ]
    },
    {
      "page": "loadEnrichResults",
      "title": "load Input data (enrichKEGG object)",
      "topics": [
        "loadEnrichResults"
      ]
    },
    {
      "page": "loadGeneData",
      "title": "load Input data (enrichKEGG object)",
      "topics": [
        "loadGeneData"
      ]
    },
    {
      "page": "lrt_yeast",
      "title": "An example DGELRT object is provided in the `lrt_yeast` dataset. This object contains the results of a differential gene expression analysis using the edgeR package. logFC values correspond to the effect of a gene knockout on response to ethanol stress in yeast.",
      "topics": [
        "lrt_yeast"
      ]
    },
    {
      "page": "plotParalogs",
      "title": "Full Workflow for KEGG Pathway Visualization",
      "topics": [
        "plotParalogs"
      ]
    },
    {
      "page": "process_ggkegg",
      "title": "Process ggkegg Data for Visualization",
      "topics": [
        "process_ggkegg"
      ]
    }
  ],
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