{
  "_id": "6a193f79acfb0bcc41dd6086",
  "Package": "GeneTonic",
  "Title": "Enjoy Analyzing And Integrating The Results From Differential\nExpression Analysis And Functional Enrichment Analysis",
  "Version": "3.6.0",
  "Date": "2025-09-23",
  "Authors@R": "c(\nperson(\ngiven = \"Federico\", family = \"Marini\", role = c(\"aut\", \"cre\"),\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n),\nperson(\ngiven = \"Annekathrin\", family = \"Nedwed\", role = c(\"aut\"),\nemail = \"anneludt@uni-mainz.de\", comment = c(ORCID = \"0000-0002-2475-4945\")\n),\nperson(\ngiven = \"Edoardo\", family = \"Filippi\", role = c(\"ctb\"),\nemail = \"edoardo.filippi@uni-mainz.de\", comment = c(ORCID = \"0009-0003-9858-0137\")\n)\n)",
  "Description": "This package provides functionality to combine the\nexisting pieces of the transcriptome data and results, making\nit easier to generate insightful observations and hypothesis.\nIts usage is made easy with a Shiny application, combining the\nbenefits of interactivity and reproducibility e.g. by capturing\nthe features and gene sets of interest highlighted during the\nlive session, and creating an HTML report as an artifact where\ntext, code, and output coexist. Using the GeneTonicList as a\nstandardized container for all the required components, it is\npossible to simplify the generation of multiple visualizations\nand summaries.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/federicomarini/GeneTonic",
  "BugReports": "https://github.com/federicomarini/GeneTonic/issues",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
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  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:46 UTC",
  "RemoteUrl": "https://github.com/bioc/GeneTonic",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "57c6b8dda66e9af1734c280fa1027c830c92aa17",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:31:03 UTC",
    "User": "root"
  },
  "Author": "Federico Marini [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3252-7758>),\nAnnekathrin Nedwed [aut] (ORCID:\n<https://orcid.org/0000-0002-2475-4945>),\nEdoardo Filippi [ctb] (ORCID: <https://orcid.org/0009-0003-9858-0137>)",
  "Maintainer": "Federico Marini <marinif@uni-mainz.de>",
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  "_created": "2026-05-29T06:31:03.000Z",
  "_published": "2026-05-29T07:25:45.803Z",
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    "manual.pdf"
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  "_exports": [
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    "checkup_GeneTonic",
    "checkup_gtl",
    "cluster_markov",
    "create_jaccard_matrix",
    "create_kappa_matrix",
    "create_upsetdata",
    "describe_gtl",
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    "distill_enrichment",
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    "enrichment_map",
    "export_for_iSEE",
    "export_to_sif",
    "gene_plot",
    "geneinfo_2_html",
    "GeneTonic",
    "GeneTonic_list",
    "GeneTonicList",
    "get_aggrscores",
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    "go_2_html",
    "gs_alluvial",
    "gs_dendro",
    "gs_fuzzyclustering",
    "gs_heatmap",
    "gs_horizon",
    "gs_mds",
    "gs_radar",
    "gs_sankey",
    "gs_scores",
    "gs_scoresheat",
    "gs_simplify",
    "gs_spider",
    "gs_summary_heat",
    "gs_summary_overview",
    "gs_summary_overview_pair",
    "gs_upset",
    "gs_volcano",
    "happy_hour",
    "map2color",
    "overlap_coefficient",
    "overlap_jaccard_index",
    "shake_davidResult",
    "shake_enrichResult",
    "shake_enrichrResult",
    "shake_fgseaResult",
    "shake_gprofilerResult",
    "shake_gsenrichResult",
    "shake_topGOtableResult",
    "signature_volcano",
    "styleColorBar_divergent",
    "summarize_ggs_hubgenes"
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      "name": "enrichr_output_macrophage",
      "title": "A sample output from Enrichr",
      "object": "enrichr_output_macrophage",
      "file": "enrichr_output_macrophage.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "title": "A sample output from fgsea",
      "object": "fgseaRes",
      "file": "fgseaRes.RData",
      "class": [
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      ],
      "fields": [
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        "padj",
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      ],
      "rows": 7341,
      "table": true,
      "tojson": true
    },
    {
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      ],
      "fields": [],
      "table": false,
      "tojson": true
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      "title": "A sample 'DESeqResults' object",
      "object": "res_de_macrophage",
      "file": "res_de_macrophage.RData",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "topgoDE_macrophage_IFNg_vs_naive",
      "title": "A sample 'res_enrich' object",
      "object": "res_enrich_macrophage",
      "file": "res_enrich_macrophage.RData",
      "class": [
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      ],
      "fields": [
        "GO.ID",
        "Term",
        "Annotated",
        "Significant",
        "Expected",
        "Rank in p.value_classic",
        "p.value_elim",
        "p.value_classic",
        "genes"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "dot-check_pandoc",
      "title": "Check whether 'pandoc' and 'pandoc-citeproc' are available",
      "topics": [
        ".check_pandoc"
      ]
    },
    {
      "page": "check_colors",
      "title": "Check colors",
      "topics": [
        "check_colors"
      ]
    },
    {
      "page": "checkup_GeneTonic",
      "title": "Checking the input objects for GeneTonic",
      "topics": [
        "checkup_GeneTonic"
      ]
    },
    {
      "page": "checkup_gtl",
      "title": "Checking the 'gtl' input object for GeneTonic",
      "topics": [
        "checkup_gtl"
      ]
    },
    {
      "page": "cluster_markov",
      "title": "Markov Clustering (MCL) for community detection",
      "topics": [
        "cluster_markov"
      ]
    },
    {
      "page": "create_jaccard_matrix",
      "title": "Compute the overlap matrix for enrichment results",
      "topics": [
        "create_jaccard_matrix"
      ]
    },
    {
      "page": "create_kappa_matrix",
      "title": "Compute the kappa matrix for enrichment results",
      "topics": [
        "create_kappa_matrix"
      ]
    },
    {
      "page": "create_upsetdata",
      "title": "Create a geneset upset dataset",
      "topics": [
        "create_upsetdata"
      ]
    },
    {
      "page": "deprecated",
      "title": "Deprecated functions in GeneTonic",
      "topics": [
        "deprecated"
      ]
    },
    {
      "page": "describe_gtl",
      "title": "Describe a GeneTonic list",
      "topics": [
        "describe_gtl"
      ]
    },
    {
      "page": "deseqresult2df",
      "title": "Generate a table from the 'DESeq2' results",
      "topics": [
        "deseqresult2df"
      ]
    },
    {
      "page": "distill_enrichment",
      "title": "Distill enrichment results",
      "topics": [
        "distill_enrichment"
      ]
    },
    {
      "page": "editor_to_vector_sanitized",
      "title": "Extract vectors from editor content",
      "topics": [
        "editor_to_vector_sanitized"
      ]
    },
    {
      "page": "enhance_table",
      "title": "Visually enhances a functional enrichment result table",
      "topics": [
        "enhance_table"
      ]
    },
    {
      "page": "enrichment_map",
      "title": "Creates an enrichment map for the results of functional enrichment",
      "topics": [
        "enrichment_map"
      ]
    },
    {
      "page": "enrichr_output_macrophage",
      "title": "A sample output from Enrichr",
      "concept": [
        "pathway-analysis-results"
      ],
      "topics": [
        "enrichr_output_macrophage"
      ]
    },
    {
      "page": "export_for_iSEE",
      "title": "export_for_iSEE",
      "topics": [
        "export_for_iSEE"
      ]
    },
    {
      "page": "export_to_sif",
      "title": "Export to sif",
      "topics": [
        "export_to_sif"
      ]
    },
    {
      "page": "fgseaRes",
      "title": "A sample output from fgsea",
      "concept": [
        "pathway-analysis-results\n\n\n\nDetails on how this object has been created are included in the \nlist(\"create_gt_data.R\")\n\n\nscript, included in the \nlist(\"scripts\")\n folder of the \nlist(\"GeneTonic\")\n package."
      ],
      "topics": [
        "fgseaRes"
      ]
    },
    {
      "page": "gene_plot",
      "title": "Plot expression values for a gene",
      "topics": [
        "gene_plot"
      ]
    },
    {
      "page": "geneinfo_2_html",
      "title": "Information on a gene",
      "topics": [
        "geneinfo_2_html"
      ]
    },
    {
      "page": "GeneTonic",
      "title": "GeneTonic",
      "topics": [
        "GeneTonic"
      ]
    },
    {
      "page": "GeneTonicList",
      "title": "Create a GeneTonicList object",
      "topics": [
        "GeneTonicList",
        "GeneTonic_list"
      ]
    },
    {
      "page": "get_aggrscores",
      "title": "Compute aggregated scores for gene sets",
      "topics": [
        "get_aggrscores"
      ]
    },
    {
      "page": "get_expression_values",
      "title": "Get expression values",
      "topics": [
        "get_expression_values"
      ]
    },
    {
      "page": "ggs_backbone",
      "title": "Extract the backbone for the gene-geneset graph",
      "topics": [
        "ggs_backbone"
      ]
    },
    {
      "page": "ggs_graph",
      "title": "Construct a gene-geneset-graph",
      "topics": [
        "ggs_graph"
      ]
    },
    {
      "page": "go_2_html",
      "title": "Information on a GeneOntology identifier",
      "topics": [
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      "page": "styleColorBar_divergent",
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      "source": "GeneTonic_manual.Rmd",
      "filename": "GeneTonic_manual.html",
      "title": "The GeneTonic User's Guide",
      "author": "Federico Marini, Annekathrin Ludt",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "All set!",
        "Using the GeneTonic functions",
        "Overview functions: genes and gene sets",
        "Summary representations",
        "Reporting",
        "Comparison between sets",
        "Miscellaneous functions",
        "Additional Information",
        "FAQs",
        "Session Info",
        "References"
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      "created": "2019-06-24 13:05:33",
      "modified": "2024-09-22 09:11:49",
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