{
  "_id": "6a1af4701d7bb097a09f8cdc",
  "Package": "GeDi",
  "Title": "Defining and visualizing the distances between different\ngenesets",
  "Version": "1.9.0",
  "Date": "2025-11-26",
  "Authors@R": "c(\nperson(\ngiven = \"Annekathrin\", family = \"Nedwed\", role = c(\"aut\", \"cre\"),\nemail = \"anneludt@uni-mainz.de\", comment = c(ORCID = \"0000-0002-2475-4945\")),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = c(\"aut\"),\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n)\n)",
  "Description": "The package provides different distances measurements to\ncalculate the difference between genesets. Based on these\nscores the genesets are clustered and visualized as graph. This\nis all presented in an interactive Shiny application for easy\nusage.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/AnnekathrinSilvia/GeDi",
  "BugReports": "https://github.com/AnnekathrinSilvia/GeDi/issues",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "biocViews": "GUI, GeneSetEnrichment, Software, Transcription, RNASeq,\nVisualization, Clustering, Pathways, ReportWriting, GO, KEGG,\nReactome, ShinyApps",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:56 UTC",
  "RemoteUrl": "https://github.com/bioc/GeDi",
  "RemoteRef": "HEAD",
  "RemoteSha": "286938904be5223236bbce26539e000f8e07b10c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:44:08 UTC",
    "User": "root"
  },
  "Author": "Annekathrin Nedwed [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2475-4945>),\nFederico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)",
  "Maintainer": "Annekathrin Nedwed <anneludt@uni-mainz.de>",
  "MD5sum": "6755c324b30a9b8b8e26a81d7685867c",
  "_user": "bioc",
  "_type": "src",
  "_file": "GeDi_1.9.0.tar.gz",
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  "_created": "2026-05-30T09:44:08.000Z",
  "_published": "2026-05-30T14:30:08.629Z",
  "_jobs": [
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  "_bioccheck": {
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    "warning": 1,
    "note": 9
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676223852",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GeDi",
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    "id": "286938904be5223236bbce26539e000f8e07b10c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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  "_maintainer": {
    "name": "Annekathrin Nedwed",
    "email": "anneludt@uni-mainz.de",
    "orcid": "0000-0002-2475-4945"
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  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
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      "role": "Imports"
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      "package": "wordcloud2",
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      "package": "simona",
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    },
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    },
    {
      "package": "ReactomePA",
      "role": "Suggests"
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    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
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    {
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 2
    },
    {
      "week": "2025-46",
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    {
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    },
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  ],
  "_topics": [
    "gui",
    "genesetenrichment",
    "software",
    "transcription",
    "rnaseq",
    "visualization",
    "clustering",
    "pathways",
    "reportwriting",
    "go",
    "kegg",
    "reactome",
    "shinyapps"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "federicomarini",
      "count": 102,
      "uuid": 7447478
    },
    {
      "user": "annekathrinsilvia",
      "count": 34,
      "uuid": 33468358
    },
    {
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      "count": 8,
      "uuid": 1744257
    },
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  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 249,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GeDi"
  },
  "_devurl": "https://github.com/annekathrinsilvia/gedi",
  "_searchresults": 76,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GeDi.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/annekathrinsilvia/gedi",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".cluster_markov",
    ".map_to_color",
    "buildClusterGraph",
    "buildGraph",
    "buildHistogramData",
    "checkInclusion",
    "clustering",
    "distanceDendro",
    "distanceHeatmap",
    "enrichmentWordcloud",
    "fuzzyClustering",
    "GeDi",
    "getAdjacencyMatrix",
    "getAnnotation",
    "getBipartiteGraph",
    "getClusterAdjacencyMatrix",
    "getGenes",
    "getGraphTitle",
    "getId",
    "getInteractionScore",
    "getJaccardMatrix",
    "getKappaMatrix",
    "getMeetMinMatrix",
    "getpMMMatrix",
    "getPPI",
    "getSorensenDiceMatrix",
    "getStringDB",
    "goDistance",
    "gsHistogram",
    "kMeansClustering",
    "kNN_clustering",
    "louvainClustering",
    "markovClustering",
    "pamClustering",
    "path_to_GeDi",
    "pMMlocal",
    "prepareGenesetData",
    "seedFinding"
  ],
  "_datasets": [
    {
      "name": "macrophage_KEGG_example",
      "title": "A sample input RData file",
      "object": "macrophage_KEGG_example",
      "file": "macrophage_KEGG_example.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Description",
        "GeneRatio",
        "BgRatio",
        "pvalue",
        "p.adjust",
        "qvalue",
        "geneID",
        "Count"
      ],
      "rows": 337,
      "table": true,
      "tojson": true
    },
    {
      "name": "macrophage_Reactome_example",
      "title": "A sample input RData file",
      "object": "macrophage_Reactome_example",
      "file": "macrophage_Reactome_example.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Description",
        "GeneRatio",
        "BgRatio",
        "pvalue",
        "p.adjust",
        "qvalue",
        "geneID",
        "Count"
      ],
      "rows": 1561,
      "table": true,
      "tojson": true
    },
    {
      "name": "macrophage_topGO_example",
      "title": "A sample input RData file",
      "object": "macrophage_topGO_example",
      "file": "macrophage_topGO_example.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genesets",
        "Term",
        "Annotated",
        "Significant",
        "Expected",
        "Rank in p.value_classic",
        "p.value_elim",
        "p.value_classic",
        "Genes"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "macrophage_topGO_example_small",
      "title": "A small sample input RData file",
      "object": "macrophage_topGO_example_small",
      "file": "macrophage_topGO_example_small.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genesets",
        "Term",
        "Annotated",
        "Significant",
        "Expected",
        "Rank in p.value_classic",
        "p.value_elim",
        "p.value_classic",
        "Genes"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    },
    {
      "name": "ppi_macrophage_topGO_example_small",
      "title": "PPI",
      "object": "ppi_macrophage_topGO_example_small",
      "file": "ppi_macrophage_topGO_example_small.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene1",
        "Gene2",
        "combined_score"
      ],
      "rows": 20458,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_geneset",
      "title": "A sample input text file",
      "object": "sample_geneset",
      "file": "sample_geneset.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Geneset",
        "Genes",
        "qvalue"
      ],
      "rows": 193,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_geneset_broken",
      "title": "A broken input text file",
      "object": "sample_geneset_broken",
      "file": "sample_geneset_broken.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genesets",
        "qvalue"
      ],
      "rows": 193,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_geneset_empty",
      "title": "An empty input text file",
      "object": "sample_geneset_empty",
      "file": "sample_geneset_empty.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genesets",
        "Genes"
      ],
      "rows": 0,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_geneset_small",
      "title": "A small sample input text file",
      "object": "sample_geneset_small",
      "file": "sample_geneset_small.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genesets",
        "Genes",
        "qvalue"
      ],
      "rows": 29,
      "table": true,
      "tojson": true
    },
    {
      "name": "scores_macrophage_topGO_example_small",
      "title": "Sample scores",
      "object": "scores_macrophage_topGO_example_small",
      "file": "scores_macrophage_topGO_example_small.RData",
      "class": [
        "dgCMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-checkGenesets",
      "title": "Check genesets format",
      "topics": [
        ".checkGenesets"
      ]
    },
    {
      "page": "dot-checkGTL",
      "title": "Check GeneTonic List format",
      "topics": [
        ".checkGTL"
      ]
    },
    {
      "page": "dot-checkPPI",
      "title": "Check PPI format",
      "topics": [
        ".checkPPI"
      ]
    },
    {
      "page": "dot-checkScores",
      "title": "Check distance scores format",
      "topics": [
        ".checkScores"
      ]
    },
    {
      "page": "dot-cluster_markov",
      "title": "Markov Clustering (MCL) for community detection",
      "topics": [
        ".cluster_markov"
      ]
    },
    {
      "page": "dot-filterGenesets",
      "title": "Filter Genesets from the input data",
      "topics": [
        ".filterGenesets"
      ]
    },
    {
      "page": "dot-findSeparator",
      "title": "Make an educated guess on the separator character",
      "topics": [
        ".findSeparator"
      ]
    },
    {
      "page": "dot-getClusterDatatable",
      "title": "Map each geneset to the cluster it belongs",
      "topics": [
        ".getClusterDatatable"
      ]
    },
    {
      "page": "dot-getGenesetDescriptions",
      "title": "Get gene set descriptions",
      "topics": [
        ".getGenesetDescriptions"
      ]
    },
    {
      "page": "dot-getNumberCores",
      "title": "Determine the number of cores to use for a function",
      "topics": [
        ".getNumberCores"
      ]
    },
    {
      "page": "dot-graphMetricsGenesetsDT",
      "title": "Generate a 'data.frame' of graph metrics",
      "topics": [
        ".graphMetricsGenesetsDT"
      ]
    },
    {
      "page": "dot-map_to_color",
      "title": "Maps numeric values to color values",
      "topics": [
        ".map_to_color"
      ]
    },
    {
      "page": "dot-sepguesser",
      "title": "Make an educated guess on the separator character",
      "topics": [
        ".sepguesser"
      ]
    },
    {
      "page": "buildClusterGraph",
      "title": "Build a cluster graph",
      "topics": [
        "buildClusterGraph"
      ]
    },
    {
      "page": "buildGraph",
      "title": "Construct a graph",
      "topics": [
        "buildGraph"
      ]
    },
    {
      "page": "buildHistogramData",
      "title": "Prepare data for 'gsHistogram()'.",
      "topics": [
        "buildHistogramData"
      ]
    },
    {
      "page": "checkInclusion",
      "title": "Check for subset inclusion",
      "topics": [
        "checkInclusion"
      ]
    },
    {
      "page": "clustering",
      "title": "Cluster genesets.",
      "topics": [
        "clustering"
      ]
    },
    {
      "page": "deprecated",
      "title": "Deprecated functions in GeDi",
      "topics": [
        "deprecated"
      ]
    },
    {
      "page": "distanceDendro",
      "title": "Plot a dendrogram",
      "topics": [
        "distanceDendro"
      ]
    },
    {
      "page": "distanceHeatmap",
      "title": "Plot a heatmap",
      "topics": [
        "distanceHeatmap"
      ]
    },
    {
      "page": "enrichmentWordcloud",
      "title": "Visualize the results of an enrichment analysis as word cloud",
      "topics": [
        "enrichmentWordcloud"
      ]
    },
    {
      "page": "fuzzyClustering",
      "title": "Find cluster from initial seeds",
      "topics": [
        "fuzzyClustering"
      ]
    },
    {
      "page": "GeDi",
      "title": "GeDi main function",
      "topics": [
        "GeDi"
      ]
    },
    {
      "page": "getAdjacencyMatrix",
      "title": "Construct an adjacency matrix",
      "topics": [
        "getAdjacencyMatrix"
      ]
    },
    {
      "page": "getAnnotation",
      "title": "Get the annotation of a 'STRINGdb' object",
      "topics": [
        "getAnnotation"
      ]
    },
    {
      "page": "getBipartiteGraph",
      "title": "Construct a bipartite graph",
      "topics": [
        "getBipartiteGraph"
      ]
    },
    {
      "page": "getClusterAdjacencyMatrix",
      "title": "Construct an adjacency matrix",
      "topics": [
        "getClusterAdjacencyMatrix"
      ]
    },
    {
      "page": "getGenes",
      "title": "Split string of genes",
      "topics": [
        "getGenes"
      ]
    },
    {
      "page": "getGraphTitle",
      "title": "Build up the node title",
      "topics": [
        "getGraphTitle"
      ]
    },
    {
      "page": "getId",
      "title": "Get NCBI ID",
      "topics": [
        "getId"
      ]
    },
    {
      "page": "getInteractionScore",
      "title": "Calculate interaction score for two genesets",
      "topics": [
        "getInteractionScore"
      ]
    },
    {
      "page": "getJaccardMatrix",
      "title": "Get Matrix of Jaccard distances",
      "topics": [
        "getJaccardMatrix"
      ]
    },
    {
      "page": "getKappaMatrix",
      "title": "Get Matrix of Kappa distances",
      "topics": [
        "getKappaMatrix"
      ]
    },
    {
      "page": "getMeetMinMatrix",
      "title": "Get Matrix of Meet-Min distances",
      "topics": [
        "getMeetMinMatrix"
      ]
    },
    {
      "page": "getpMMMatrix",
      "title": "Calculate the pMM distance",
      "topics": [
        "getpMMMatrix"
      ]
    },
    {
      "page": "getPPI",
      "title": "Download Protein-Protein Interaction (PPI)",
      "topics": [
        "getPPI"
      ]
    },
    {
      "page": "getSorensenDiceMatrix",
      "title": "Get Matrix of Sorensen-Dice distances",
      "topics": [
        "getSorensenDiceMatrix"
      ]
    },
    {
      "page": "getStringDB",
      "title": "Get the STRING db entry of a species",
      "topics": [
        "getStringDB"
      ]
    },
    {
      "page": "goDistance",
      "title": "Calculate similarity of GO terms",
      "topics": [
        "goDistance"
      ]
    },
    {
      "page": "gsHistogram",
      "title": "Create a histogram plot for gene set sizes",
      "topics": [
        "gsHistogram"
      ]
    },
    {
      "page": "kMeansClustering",
      "title": "Calculate clusters based on kMeans clustering",
      "topics": [
        "kMeansClustering"
      ]
    },
    {
      "page": "kNN_clustering",
      "title": "Calculate clusters based on kNN clustering",
      "topics": [
        "kNN_clustering"
      ]
    },
    {
      "page": "louvainClustering",
      "title": "Cluster genesets using Louvain clustering.",
      "topics": [
        "louvainClustering"
      ]
    },
    {
      "page": "macrophage_KEGG_example",
      "title": "A sample input RData file",
      "topics": [
        "macrophage_KEGG_example"
      ]
    },
    {
      "page": "macrophage_Reactome_example",
      "title": "A sample input RData file",
      "topics": [
        "macrophage_Reactome_example"
      ]
    },
    {
      "page": "macrophage_topGO_example",
      "title": "A sample input RData file",
      "topics": [
        "macrophage_topGO_example"
      ]
    },
    {
      "page": "macrophage_topGO_example_small",
      "title": "A small sample input RData file",
      "topics": [
        "macrophage_topGO_example_small"
      ]
    },
    {
      "page": "markovClustering",
      "title": "Cluster genesets using Markov clustering.",
      "topics": [
        "markovClustering"
      ]
    },
    {
      "page": "pamClustering",
      "title": "Calculate clusters based on PAM clustering",
      "topics": [
        "pamClustering"
      ]
    },
    {
      "page": "path_to_GeDi",
      "title": "Prepare enrichment analysis output data for GeDi",
      "topics": [
        "path_to_GeDi"
      ]
    },
    {
      "page": "pMMlocal",
      "title": "Calculate local pMM distance",
      "topics": [
        "pMMlocal"
      ]
    },
    {
      "page": "ppi_macrophage_topGO_example_small",
      "title": "PPI",
      "topics": [
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      ]
    },
    {
      "page": "prepareGenesetData",
      "title": "Split string of genes",
      "topics": [
        "prepareGenesetData"
      ]
    },
    {
      "page": "sample_geneset",
      "title": "A sample input text file",
      "topics": [
        "sample_geneset"
      ]
    },
    {
      "page": "sample_geneset_broken",
      "title": "A broken input text file",
      "topics": [
        "sample_geneset_broken"
      ]
    },
    {
      "page": "sample_geneset_empty",
      "title": "An empty input text file",
      "topics": [
        "sample_geneset_empty"
      ]
    },
    {
      "page": "sample_geneset_small",
      "title": "A small sample input text file",
      "topics": [
        "sample_geneset_small"
      ]
    },
    {
      "page": "scores_macrophage_topGO_example_small",
      "title": "Sample scores",
      "topics": [
        "scores_macrophage_topGO_example_small"
      ]
    },
    {
      "page": "seedFinding",
      "title": "Find clustering seeds",
      "topics": [
        "seedFinding"
      ]
    }
  ],
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    "shinycssloaders",
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    "sqldf",
    "STRINGdb",
    "stringi",
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    "tibble",
    "tidyr",
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    "tinytex",
    "tm",
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    "vctrs",
    "viridisLite",
    "visNetwork",
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  "_vignettes": [
    {
      "source": "GeDi_manual.Rmd",
      "filename": "GeDi_manual.html",
      "title": "The GeDi User's Guide",
      "author": "Annekathrin Silvia Nedwed, Federico Marini",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "All set!",
        "Description of the GeDi user interface",
        "Header (navbar)",
        "Sidebar",
        "Body",
        "The GeDi functionality",
        "The Welcome panel",
        "The Data Input panel",
        "The Distance Scores panel",
        "The Clustering Graph panel",
        "The Report panel",
        "Additional Information",
        "Additional example data",
        "FAQs",
        "Session Info",
        "References"
      ],
      "created": "2022-02-09 15:41:25",
      "modified": "2025-11-12 10:53:24",
      "commits": 39
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  "_score": 5.9599948383284165,
  "_indexed": true,
  "_nocasepkg": "gedi",
  "_universes": [
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