{
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  "Package": "DeSciDe",
  "Type": "Package",
  "Title": "Tool for Unbiased Literature Searching and Gene List Curation",
  "Version": "1.0.3",
  "Authors@R": "person(\"Cameron\", \"Douglas\", email = \"camerondouglas@ufl.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2334-1652\"))",
  "Description": "Designed for genomic and proteomic data analysis, enabling\nunbiased PubMed searching, protein interaction network\nvisualization, and comprehensive data summarization. This\npackage aims to help users identify novel targets within their\ndata sets based on protein network interactions and publication\nprecedence of target's association with research context based\non literature precedence. Methods in this package are described\nin detail in: Douglas et al. (2025)\n<https://doi.org/10.1039/D5MO00160A>. Key functionalities of\nthis package also leverage methodologies from previous works,\nsuch as: - Szklarczyk et al. (2023) <doi:10.1093/nar/gkac1000>\n- Winter (2017) <doi:10.32614/RJ-2017-066>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
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  "BugReports": "https://github.com/camdouglas/DeSciDe/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
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  "Repository": "https://camdouglas.r-universe.dev",
  "Date/Publication": "2026-04-08 22:53:44 UTC",
  "RemoteUrl": "https://github.com/camdouglas/descide",
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    "User": "root"
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  "Maintainer": "Cameron Douglas <camerondouglas@ufl.edu>",
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    "author": "Cameron Douglas <cdouglas105@gmail.com>",
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 2
    },
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    }
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  "_stars": 1,
  "_contributors": [
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      "count": 66,
      "uuid": 120063313
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DeSciDe"
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    "extra/citation.json",
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      "date": "2026-04-09"
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    "combine_summary",
    "descide",
    "plot_clustering",
    "plot_connectivity_precedence",
    "plot_heatmap",
    "plot_string_network",
    "rank_search_results",
    "search_pubmed",
    "search_string_db",
    "single_pubmed_search"
  ],
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    {
      "page": "combine_summary",
      "title": "Combine PubMed and STRING Metrics",
      "topics": [
        "combine_summary"
      ]
    },
    {
      "page": "descide",
      "title": "Run DeSciDe pipeline",
      "topics": [
        "descide"
      ]
    },
    {
      "page": "plot_clustering",
      "title": "Plot STRING Interactions",
      "topics": [
        "plot_clustering"
      ]
    },
    {
      "page": "plot_connectivity_precedence",
      "title": "Plot Connectivity vs. Precedence",
      "topics": [
        "plot_connectivity_precedence"
      ]
    },
    {
      "page": "plot_heatmap",
      "title": "Plot Heatmap",
      "topics": [
        "plot_heatmap"
      ]
    },
    {
      "page": "plot_string_network",
      "title": "Plot STRING Network",
      "topics": [
        "plot_string_network"
      ]
    },
    {
      "page": "rank_search_results",
      "title": "Rank Search Results",
      "topics": [
        "rank_search_results"
      ]
    },
    {
      "page": "search_pubmed",
      "title": "Search PubMed with Multiple Genes and Terms",
      "topics": [
        "search_pubmed"
      ]
    },
    {
      "page": "search_string_db",
      "title": "Search STRING Database",
      "topics": [
        "search_string_db"
      ]
    },
    {
      "page": "single_pubmed_search",
      "title": "Search PubMed",
      "topics": [
        "single_pubmed_search"
      ]
    }
  ],
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      "source": "DeSciDe-vignette.Rmd",
      "filename": "DeSciDe-vignette.html",
      "title": "DeSciDe Vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "DeSciDe (Deciphering Scientific Discoveries)",
        "Example Usage of DeSciDe",
        "Results Expected from DeSciDe",
        "Table",
        "Heatmap",
        "STRING Network",
        "Clustering",
        "Connectivity vs. Precedence",
        "Modifications to DeSciDe Search",
        "[PubMed Ranking Method: Important]",
        "[Modifications to STRING Search]",
        "[Modifications to DeSciDe Classifications]",
        "[Exporting Tables and Graphs]",
        "All Functions Available for DeSciDe",
        "Function to run entire pipeline",
        "Function to run PubMed search",
        "Function to plot heatmap",
        "Function to search STRING",
        "Function to plot STRING network",
        "Function to plot STRING clustering metrics",
        "Function to create summary file and classify genes based on ranks.",
        "Function to plot connectivity vs. precedence."
      ],
      "created": "2025-04-07 21:08:25",
      "modified": "2025-08-12 19:14:27",
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