{
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  "Title": "Interactive Exploration of GSEA by the GOAT Method",
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  "Authors@R": "person(\"Maurits\", \"Unkel\",\nrole = c(\"aut\", \"cre\", \"fnd\", \"cph\"),\nemail = \"mauritsunkel@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1920-6001\"))",
  "Description": "Geneset Ordinal Association Test Enrichment Analysis\n(GOATEA) provides a 'Shiny' interface with interactive\nvisualizations and utility functions for performing and\nexploring automated gene set enrichment analysis using the\n'GOAT' package. 'GOATEA' is designed to support large-scale and\nuser-friendly enrichment workflows across multiple gene lists\nand comparisons, with flexible plotting and output options.\nVisualizations pre-enrichment include interactive 'Volcano' and\n'UpSet' (overlap) plots. Visualizations post-enrichment include\ninteractive geneset dotplot, geneset treeplot, gene-effectsize\nheatmap, gene-geneset heatmap and 'STRING' database of\nprotein-protein-interactions network graph. 'GOAT' reference:\nFrank Koopmans (2024) <doi:10.1038/s42003-024-06454-5>.",
  "URL": "https://github.com/mauritsunkel/goatea,\nhttps://mauritsunkel.github.io/goatea/",
  "BugReports": "https://github.com/mauritsunkel/goatea/issues",
  "License": "Apache License (>= 2)",
  "Encoding": "UTF-8",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:29 UTC",
  "RemoteUrl": "https://github.com/bioc/goatea",
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  "Packaged": {
    "Date": "2026-05-30 08:22:06 UTC",
    "User": "root"
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  "Author": "Maurits Unkel [aut, cre, fnd, cph] (ORCID:\n<https://orcid.org/0000-0003-1920-6001>)",
  "Maintainer": "Maurits Unkel <mauritsunkel@gmail.com>",
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  "_published": "2026-05-30T11:57:46.449Z",
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    "functionalgenomics",
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    "calculate_geneSetRatio",
    "colorify",
    "file_extension",
    "filter_enrichment",
    "get_base_folder",
    "get_ppigraph",
    "get_string_ppi",
    "get_terms_by_keywords",
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        "log2fc",
        "effectsize",
        "pvalue",
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        "entrez_id",
        "gene",
        "signif"
      ],
      "rows": 3935,
      "table": true,
      "tojson": true
    },
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      "class": [
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      ],
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        "effectsize",
        "pvalue",
        "pvalue_adjust",
        "hgnc_id",
        "hgnc_symbol",
        "entrez_id",
        "gene",
        "signif"
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      "table": true,
      "tojson": true
    },
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      "title": "An example enrichment",
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      "file": "example_enrichment.rda",
      "class": [
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        "tbl",
        "data.frame"
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      "fields": [
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        "source_version",
        "id",
        "name",
        "parent_id",
        "ngenes_input",
        "ngenes",
        "ngenes_signif",
        "genes",
        "genes_signif",
        "score_type",
        "pvalue",
        "zscore",
        "pvalue_adjust",
        "signif",
        "score_oddsratio",
        "symbol"
      ],
      "rows": 10,
      "table": true,
      "tojson": false
    },
    {
      "name": "example_genelist",
      "title": "An example genelist",
      "object": "example_genelist",
      "file": "example_genelist.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "symbol",
        "gene",
        "pvalue",
        "effectsize",
        "signif"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_genes_overview",
      "title": "An example genes overview",
      "object": "example_genes_overview",
      "file": "example_genes_overview.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "gene",
        "symbol",
        "A_efsi",
        "A_pval",
        "B_efsi",
        "B_pval",
        "A_perc",
        "B_perc",
        "genelist_overlap",
        "A_geneSetRatio",
        "A_SS_geneSetRatio",
        "B_geneSetRatio",
        "B_SS_geneSetRatio"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_genesets",
      "title": "Example genesets",
      "object": "example_genesets",
      "file": "example_genesets.rda",
      "class": [
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        "tbl",
        "data.frame"
      ],
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        "id",
        "name",
        "parent_id",
        "ngenes_input",
        "ngenes",
        "ngenes_signif",
        "genes",
        "genes_signif"
      ],
      "rows": 10,
      "table": true,
      "tojson": false
    },
    {
      "name": "example_ppi_data",
      "title": "An example ppi data",
      "object": "example_ppi_data",
      "file": "example_ppi_data.rda",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
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        "to_symbol",
        "combined_score",
        "from",
        "to"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculate_geneSetRatio",
      "title": "Calculate geneSetRatio per gene per enrichment contrast",
      "topics": [
        "calculate_geneSetRatio"
      ]
    },
    {
      "page": "colorify",
      "title": "Create and/or modify color/gradient palettes",
      "topics": [
        "colorify"
      ]
    },
    {
      "page": "colorify_map",
      "title": "Colorify colorRamp between colors mapping to breakpoint values",
      "topics": [
        "colorify_map"
      ]
    },
    {
      "page": "display_palettes",
      "title": "Display R grDevices palettes",
      "topics": [
        "display_palettes"
      ]
    },
    {
      "page": "example_Colameo_MS",
      "title": "Example Colameo MS data",
      "topics": [
        "example_Colameo_MS"
      ]
    },
    {
      "page": "example_Colameo_RNA",
      "title": "Example Colameo RNA data",
      "topics": [
        "example_Colameo_RNA"
      ]
    },
    {
      "page": "example_enrichment",
      "title": "An example enrichment",
      "topics": [
        "example_enrichment"
      ]
    },
    {
      "page": "example_genelist",
      "title": "An example genelist",
      "topics": [
        "example_genelist"
      ]
    },
    {
      "page": "example_genes_overview",
      "title": "An example genes overview",
      "topics": [
        "example_genes_overview"
      ]
    },
    {
      "page": "example_genesets",
      "title": "Example genesets",
      "topics": [
        "example_genesets"
      ]
    },
    {
      "page": "example_ppi_data",
      "title": "An example ppi data",
      "topics": [
        "example_ppi_data"
      ]
    },
    {
      "page": "file_extension",
      "title": "Get file extension",
      "topics": [
        "file_extension"
      ]
    },
    {
      "page": "filter_enrichment",
      "title": "Filter enrichment",
      "topics": [
        "filter_enrichment"
      ]
    },
    {
      "page": "get_base_folder",
      "title": "Set base folder",
      "topics": [
        "get_base_folder"
      ]
    },
    {
      "page": "get_ppigraph",
      "title": "Get PPI igraph",
      "topics": [
        "get_ppigraph"
      ]
    },
    {
      "page": "get_string_ppi",
      "title": "Get STRING database Protein-Protein Interactions",
      "topics": [
        "get_string_ppi"
      ]
    },
    {
      "page": "get_terms_by_keywords",
      "title": "Get term names by searching with (partial) keywords",
      "topics": [
        "get_terms_by_keywords"
      ]
    },
    {
      "page": "get_visNetwork",
      "title": "Get visNetwork graph",
      "topics": [
        "get_visNetwork"
      ]
    },
    {
      "page": "goatea_server",
      "title": "Server for goatea package",
      "topics": [
        "goatea_server"
      ]
    },
    {
      "page": "goatea_ui",
      "title": "UI for GOATEA package",
      "topics": [
        "goatea_ui"
      ]
    },
    {
      "page": "hexcolor2rgba",
      "title": "Hex code colors to rgba format",
      "topics": [
        "hexcolor2rgba"
      ]
    },
    {
      "page": "palette_name_mapping",
      "title": "Palette original name mapping",
      "topics": [
        "palette_name_mapping"
      ]
    },
    {
      "page": "plot_ComplexHeatmap",
      "title": "Plot ComplexHeatmap",
      "topics": [
        "plot_ComplexHeatmap"
      ]
    },
    {
      "page": "plot_EnhancedVolcano",
      "title": "Plot EnhancedVolcano",
      "topics": [
        "plot_EnhancedVolcano"
      ]
    },
    {
      "page": "plot_gene_effectsize_ComplexHeatmap",
      "title": "Plot gene2effectsize ComplexHeatmap",
      "topics": [
        "plot_gene_effectsize_ComplexHeatmap"
      ]
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