{
  "_id": "6a43c4b258db26aa3c359531",
  "Package": "pathfindR.data",
  "Title": "Data Package for 'pathfindR'",
  "Version": "2.2.0",
  "Authors@R": "c(person(\"Ege\", \"Ulgen\",\nrole = c(\"cre\", \"cph\"),\nemail = \"egeulgen@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2090-3621\")),\nperson(\"Ozan\", \"Ozisik\",\nrole = \"aut\",\nemail = \"ozanytu@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5980-8002\")))",
  "Maintainer": "Ege Ulgen <egeulgen@gmail.com>",
  "Description": "This is a data-only package, containing data needed to run\nthe CRAN package 'pathfindR', a package for enrichment analysis\nutilizing active subnetworks. This package contains\nprotein-protein interaction network data, data related to gene\nsets and example input/output data.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/egeulgen/pathfindR.data",
  "BugReports": "https://github.com/egeulgen/pathfindR.data/issues",
  "Config/roxygen2/version": "8.0.0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-30 13:26:11 UTC",
    "User": "root"
  },
  "Author": "Ege Ulgen [cre, cph] (ORCID:\n<https://orcid.org/0000-0003-2090-3621>), Ozan Ozisik [aut]\n(ORCID: <https://orcid.org/0000-0001-5980-8002>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-06-30 11:58:10 UTC",
  "RemoteUrl": "https://github.com/cran/pathfindR.data",
  "RemoteRef": "HEAD",
  "RemoteSha": "dd81c4cdf7ffe26c33290fb71649d2f9c0215728",
  "MD5sum": "d2740c7cad3570679832a1e59f0942ec",
  "_user": "cran",
  "_type": "src",
  "_file": "pathfindR.data_2.2.0.tar.gz",
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  "_published": "2026-06-30T13:29:22.203Z",
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  "_status": "success",
  "_host": "GitHub-Actions",
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  "_commit": {
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    "author": "Ege Ulgen <egeulgen@gmail.com>",
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    "email": "egeulgen@gmail.com",
    "login": "egeulgen",
    "description": "MD, PhD - Bioinformatics Engineer",
    "uuid": 12850155,
    "orcid": "0000-0003-2090-3621"
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  "_registered": true,
  "_dependencies": [
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      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
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  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
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    "type": "organization",
    "name": "cran",
    "followers": 614,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
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  "_mentions": 19,
  "_devurl": "https://github.com/egeulgen/pathfindr.data",
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    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
    "extra/pathfindR.data.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/egeulgen/pathfindr.data",
  "_realowner": "egeulgen",
  "_cranurl": false,
  "_releases": [
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      "date": "2020-06-04"
    },
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      "date": "2020-09-21"
    },
    {
      "version": "1.1.1",
      "date": "2020-11-20"
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      "date": "2024-04-27"
    },
    {
      "version": "2.2.0",
      "date": "2026-06-30"
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  ],
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  "_datasets": [
    {
      "name": "biocarta_descriptions",
      "title": "BioCarta Pathways - Descriptions",
      "object": "biocarta_descriptions",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "biocarta_genes",
      "title": "BioCarta Pathways - Gene Sets",
      "object": "biocarta_genes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cell_markers_descriptions",
      "title": "Human Cell Markers - Descriptions",
      "object": "cell_markers_descriptions",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cell_markers_gsets",
      "title": "Human Cell Markers - Gene Sets",
      "object": "cell_markers_gsets",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example_active_snws",
      "title": "Example Active Subnetworks",
      "object": "example_active_snws",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "example_comparison_output",
      "title": "Second Example Output for the pathfindR Enrichment Workflow (H.sapiens. - Rheumatoid Arthritis data)",
      "object": "example_comparison_output",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Term_Description",
        "Fold_Enrichment",
        "occurrence",
        "support",
        "lowest_p",
        "highest_p",
        "Up_regulated",
        "Down_regulated"
      ],
      "rows": 43,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_custom_genesets_result",
      "title": "Custom Gene Set Enrichment Results",
      "object": "example_custom_genesets_result",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Term_Description",
        "Fold_Enrichment",
        "occurrence",
        "support",
        "lowest_p",
        "highest_p",
        "Up_regulated",
        "Down_regulated"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_experiment_matrix",
      "title": "Example Experiment Matrix for pathfindR - Enriched Term Scoring",
      "object": "example_experiment_matrix",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "GSM389703",
        "GSM389704",
        "GSM389705",
        "GSM389706",
        "GSM389707",
        "GSM389708",
        "GSM389709",
        "GSM389710",
        "GSM389711",
        "GSM389712",
        "GSM389713",
        "GSM389714",
        "GSM389715",
        "GSM389716",
        "GSM389717",
        "GSM389718",
        "GSM389719",
        "GSM389720",
        "GSM389721",
        "GSM389722",
        "GSM389723",
        "GSM389724",
        "GSM389725",
        "GSM389726",
        "GSM389727",
        "GSM389728",
        "GSM389729",
        "GSM389730",
        "GSM389731",
        "GSM389732",
        "GSM389733",
        "GSM389734",
        "GSM389735"
      ],
      "rows": 572,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_mmu_input",
      "title": "Example Input for Mus musculus - Myeloma Analysis",
      "object": "example_mmu_input",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene_Symbol",
        "FDR"
      ],
      "rows": 45,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_mmu_output",
      "title": "Example Output for Mus musculus - Myeloma Analysis",
      "object": "example_mmu_output",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Term_Description",
        "Fold_Enrichment",
        "occurrence",
        "support",
        "lowest_p",
        "highest_p",
        "Up_regulated",
        "Down_regulated"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_pathfindR_input",
      "title": "Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis (H.sapiens)",
      "object": "example_pathfindR_input",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene.symbol",
        "logFC",
        "adj.P.Val"
      ],
      "rows": 572,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_pathfindR_output",
      "title": "Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis",
      "object": "example_pathfindR_output",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Term_Description",
        "Fold_Enrichment",
        "occurrence",
        "support",
        "lowest_p",
        "highest_p",
        "Up_regulated",
        "Down_regulated"
      ],
      "rows": 138,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_pathfindR_output_clustered",
      "title": "Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis",
      "object": "example_pathfindR_output_clustered",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Term_Description",
        "Fold_Enrichment",
        "occurrence",
        "support",
        "lowest_p",
        "highest_p",
        "Up_regulated",
        "Down_regulated",
        "Cluster",
        "Status"
      ],
      "rows": 138,
      "table": true,
      "tojson": true
    },
    {
      "name": "go_all_genes",
      "title": "Gene Ontology - All Gene Ontology Gene Sets",
      "object": "go_all_genes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "kegg_descriptions",
      "title": "KEGG Pathways - Descriptions",
      "object": "kegg_descriptions",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "kegg_genes",
      "title": "KEGG Pathways - Gene Sets",
      "object": "kegg_genes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mmu_kegg_descriptions",
      "title": "Mus Musculus KEGG Pathways - Descriptions",
      "object": "mmu_kegg_descriptions",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mmu_kegg_genes",
      "title": "Mus Musculus KEGG Pathways - Gene Sets",
      "object": "mmu_kegg_genes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pathfindR.data_updates",
      "title": "Table of Data for pathfindR",
      "object": "pathfindR.data_updates",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Category",
        "Name",
        "Description",
        "Source",
        "Version",
        "Last Update"
      ],
      "rows": 29,
      "table": true,
      "tojson": true
    },
    {
      "name": "reactome_descriptions",
      "title": "Reactome Pathways - Descriptions",
      "object": "reactome_descriptions",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "reactome_genes",
      "title": "Reactome Pathways - Gene Sets",
      "object": "reactome_genes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "biocarta_descriptions",
      "title": "BioCarta Pathways - Descriptions",
      "topics": [
        "biocarta_descriptions"
      ]
    },
    {
      "page": "biocarta_genes",
      "title": "BioCarta Pathways - Gene Sets",
      "topics": [
        "biocarta_genes"
      ]
    },
    {
      "page": "cell_markers_descriptions",
      "title": "Human Cell Markers - Descriptions",
      "topics": [
        "cell_markers_descriptions"
      ]
    },
    {
      "page": "cell_markers_gsets",
      "title": "Human Cell Markers - Gene Sets",
      "topics": [
        "cell_markers_gsets"
      ]
    },
    {
      "page": "example_active_snws",
      "title": "Example Active Subnetworks",
      "topics": [
        "example_active_snws"
      ]
    },
    {
      "page": "example_comparison_output",
      "title": "Second Example Output for the pathfindR Enrichment Workflow (H.sapiens. - Rheumatoid Arthritis data)",
      "topics": [
        "example_comparison_output"
      ]
    },
    {
      "page": "example_custom_genesets_result",
      "title": "Custom Gene Set Enrichment Results",
      "topics": [
        "example_custom_genesets_result"
      ]
    },
    {
      "page": "example_experiment_matrix",
      "title": "Example Experiment Matrix for pathfindR - Enriched Term Scoring",
      "topics": [
        "example_experiment_matrix"
      ]
    },
    {
      "page": "example_mmu_input",
      "title": "Example Input for Mus musculus - Myeloma Analysis",
      "topics": [
        "example_mmu_input"
      ]
    },
    {
      "page": "example_mmu_output",
      "title": "Example Output for Mus musculus - Myeloma Analysis",
      "topics": [
        "example_mmu_output"
      ]
    },
    {
      "page": "example_pathfindR_input",
      "title": "Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis (H.sapiens)",
      "topics": [
        "example_pathfindR_input"
      ]
    },
    {
      "page": "example_pathfindR_output",
      "title": "Example Output for the pathfindR Enrichment Workflow - Rheumatoid Arthritis",
      "topics": [
        "example_pathfindR_output"
      ]
    },
    {
      "page": "example_pathfindR_output_clustered",
      "title": "Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis",
      "topics": [
        "example_pathfindR_output_clustered"
      ]
    },
    {
      "page": "go_all_genes",
      "title": "Gene Ontology - All Gene Ontology Gene Sets",
      "topics": [
        "go_all_genes"
      ]
    },
    {
      "page": "kegg_descriptions",
      "title": "KEGG Pathways - Descriptions",
      "topics": [
        "kegg_descriptions"
      ]
    },
    {
      "page": "kegg_genes",
      "title": "KEGG Pathways - Gene Sets",
      "topics": [
        "kegg_genes"
      ]
    },
    {
      "page": "mmu_kegg_descriptions",
      "title": "Mus Musculus KEGG Pathways - Descriptions",
      "topics": [
        "mmu_kegg_descriptions"
      ]
    },
    {
      "page": "mmu_kegg_genes",
      "title": "Mus Musculus KEGG Pathways - Gene Sets",
      "topics": [
        "mmu_kegg_genes"
      ]
    },
    {
      "page": "pathfindR.data_updates",
      "title": "Table of Data for pathfindR",
      "topics": [
        "pathfindR.data_updates"
      ]
    },
    {
      "page": "reactome_descriptions",
      "title": "Reactome Pathways - Descriptions",
      "topics": [
        "reactome_descriptions"
      ]
    },
    {
      "page": "reactome_genes",
      "title": "Reactome Pathways - Gene Sets",
      "topics": [
        "reactome_genes"
      ]
    }
  ],
  "_rundeps": [],
  "_score": 2.4771212547196626,
  "_indexed": false,
  "_nocasepkg": "pathfindr.data",
  "_universes": [
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