{
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  "Package": "ReactomeGSA",
  "Title": "Client for the Reactome Analysis Service for comparative\nmulti-omics gene set analysis",
  "Version": "1.27.0",
  "Authors@R": "person(\"Johannes\", \"Griss\", , \"johannes.griss@meduniwien.ac.at\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2206-9511\"))",
  "Author": "Johannes Griss [aut, cre]\n(<https://orcid.org/0000-0003-2206-9511>)",
  "Maintainer": "Johannes Griss <johannes.griss@meduniwien.ac.at>",
  "Description": "The ReactomeGSA packages uses Reactome's online analysis\nservice to perform a multi-omics gene set analysis. The main\nadvantage of this package is, that the retrieved results can be\nvisualized using REACTOME's powerful webapplication.  Since\nReactome's analysis service also uses R to perfrom the actual\ngene set analysis you will get similar results when using the\nsame packages (such as limma and edgeR) locally.  Therefore, if\nyou only require a gene set analysis, different packages are\nmore suited.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/reactome/ReactomeGSA",
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    "analyse_sc_clusters",
    "find_public_datasets",
    "generate_metadata",
    "generate_pseudo_bulk_data",
    "get_public_species",
    "get_reactome_analysis_result",
    "get_reactome_analysis_status",
    "get_reactome_data_types",
    "get_reactome_methods",
    "get_result",
    "load_public_dataset",
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    "pathways",
    "perform_reactome_analysis",
    "plot_correlations",
    "plot_gsva_heatmap",
    "plot_gsva_pathway",
    "plot_gsva_pca",
    "plot_heatmap",
    "plot_volcano",
    "print",
    "reactome_links",
    "ReactomeAnalysisRequest",
    "ReactomeAnalysisResult",
    "remove_dataset",
    "result_types",
    "set_method",
    "set_parameters",
    "show",
    "start_reactome_analysis"
  ],
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      "title": "add_dataset",
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      ],
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      ]
    },
    {
      "page": "add_dataset-ReactomeAnalysisRequest-data.frame-method",
      "title": "add_dataset - data.frame",
      "concept": [
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      "topics": [
        "add_dataset,ReactomeAnalysisRequest,data.frame-method"
      ]
    },
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      "title": "add_dataset - DGEList",
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      ],
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      ]
    },
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      "page": "add_dataset-ReactomeAnalysisRequest-EList-method",
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      "concept": [
        "add_dataset methods"
      ],
      "topics": [
        "add_dataset,ReactomeAnalysisRequest,EList-method"
      ]
    },
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      "page": "add_dataset-ReactomeAnalysisRequest-ExpressionSet-method",
      "title": "add_dataset - ExpressionSet",
      "concept": [
        "add_dataset methods"
      ],
      "topics": [
        "add_dataset,ReactomeAnalysisRequest,ExpressionSet-method"
      ]
    },
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      "page": "add_dataset-ReactomeAnalysisRequest-matrix-method",
      "title": "add_dataset - matrix",
      "concept": [
        "add_dataset methods"
      ],
      "topics": [
        "add_dataset,ReactomeAnalysisRequest,matrix-method"
      ]
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      "title": "analyse_sc_clusters",
      "topics": [
        "analyse_sc_clusters"
      ]
    },
    {
      "page": "analyse_sc_clusters-Seurat-method",
      "title": "analyse_sc_clusters - Seurat",
      "topics": [
        "analyse_sc_clusters,Seurat-method"
      ]
    },
    {
      "page": "analyse_sc_clusters-SingleCellExperiment-method",
      "title": "analyse_sc_clusters - SingleCellExperiment",
      "topics": [
        "analyse_sc_clusters,SingleCellExperiment-method"
      ]
    },
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      "page": "break_names",
      "title": "break_names",
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        "break_names"
      ]
    },
    {
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      "title": "check_reactome_url",
      "topics": [
        "check_reactome_url"
      ]
    },
    {
      "page": "checkRequestValidity",
      "title": "Check's if a ReactomeAnalysisRequest object is valid",
      "topics": [
        "checkRequestValidity"
      ]
    },
    {
      "page": "convert_reactome_result",
      "title": "Convert the Reactome JSON result to a ReactomeAnalysisResult object",
      "topics": [
        "convert_reactome_result"
      ]
    },
    {
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      "title": "Converts a data.frame to a string representation",
      "topics": [
        "data_frame_as_string"
      ]
    },
    {
      "page": "fetch_public_data",
      "title": "fetch_public_data",
      "topics": [
        "fetch_public_data"
      ]
    },
    {
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      "title": "find_public_datasets",
      "topics": [
        "find_public_datasets"
      ]
    },
    {
      "page": "generate_metadata",
      "title": "generate_metadata",
      "topics": [
        "generate_metadata"
      ]
    },
    {
      "page": "generate_metadata-data.frame-method",
      "title": "Generate metadata",
      "topics": [
        "generate_metadata,data.frame-method"
      ]
    },
    {
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        "generate_pseudo_bulk_data"
      ]
    },
    {
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      "title": "generate_pseudo_bulk_data - Seurat",
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        "generate_pseudo_bulk_data,Seurat-method"
      ]
    },
    {
      "page": "generate_pseudo_bulk_data-SingleCellExperiment-method",
      "title": "generate_pseudo_bulk_data - SingleCellExperiment",
      "topics": [
        "generate_pseudo_bulk_data,SingleCellExperiment-method"
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    },
    {
      "page": "get_dataset_loading_status",
      "title": "Retrieves the status of the submitted dataset loading request",
      "topics": [
        "get_dataset_loading_status"
      ]
    },
    {
      "page": "get_fc_for_dataset",
      "title": "get_fc_for_dataset",
      "topics": [
        "get_fc_for_dataset"
      ]
    },
    {
      "page": "get_is_sig_dataset",
      "title": "get_is_sig_dataset",
      "topics": [
        "get_is_sig_dataset"
      ]
    },
    {
      "page": "get_public_species",
      "title": "get_public_species",
      "topics": [
        "get_public_species"
      ]
    },
    {
      "page": "get_reactome_analysis_result",
      "title": "Retrieves the result of the submitted analysis using 'perform_reactome_analysis'",
      "topics": [
        "get_reactome_analysis_result"
      ]
    },
    {
      "page": "get_reactome_analysis_status",
      "title": "Retrieves the status of the submitted analysis using 'start_reactome_analysis'",
      "topics": [
        "get_reactome_analysis_status"
      ]
    },
    {
      "page": "get_reactome_data_types",
      "title": "ReactomeGSA supported data types",
      "concept": [
        "Reactome Service functions"
      ],
      "topics": [
        "get_reactome_data_types"
      ]
    },
    {
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      "title": "get_reactome_methods",
      "concept": [
        "Reactome Service functions"
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      "topics": [
        "get_reactome_methods"
      ]
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    {
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      "title": "get_result",
      "concept": [
        "ReactomeAnalysisResult functions"
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      "topics": [
        "get_result"
      ]
    },
    {
      "page": "get_result-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - get_result",
      "topics": [
        "get_result,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "is_gsva_result",
      "title": "is_gsva_result",
      "topics": [
        "is_gsva_result"
      ]
    },
    {
      "page": "load_public_dataset",
      "title": "load_public_dataset",
      "topics": [
        "load_public_dataset"
      ]
    },
    {
      "page": "names-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - names",
      "concept": [
        "ReactomeAnalysisResult functions"
      ],
      "topics": [
        "names,ReactomeAnalysisResult-method"
      ]
    },
    {
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      "title": "open_reactome",
      "concept": [
        "ReactomeAnalysisResult functions"
      ],
      "topics": [
        "open_reactome"
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    },
    {
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      "title": "open_reactome - ReactomeAnalysisResult",
      "topics": [
        "open_reactome,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "pathways",
      "title": "pathways",
      "concept": [
        "ReactomeAnalysisResult functions"
      ],
      "topics": [
        "pathways"
      ]
    },
    {
      "page": "pathways-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - pathways",
      "topics": [
        "pathways,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "perform_reactome_analysis",
      "title": "Perform a Reactome Analaysis",
      "topics": [
        "perform_reactome_analysis"
      ]
    },
    {
      "page": "plot_correlations",
      "title": "plot_correlations",
      "concept": [
        "ReactomeAnalysisResult functions"
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      "title": "plot_correlations - ReactomeAnalysisResult",
      "topics": [
        "plot_correlations,ReactomeAnalysisResult-method"
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    {
      "page": "plot_gsva_heatmap",
      "title": "plot_gsva_heatmap",
      "concept": [
        "ReactomeAnalysisResult functions"
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      "topics": [
        "plot_gsva_heatmap"
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    {
      "page": "plot_gsva_heatmap-ReactomeAnalysisResult-method",
      "title": "plot_gsva_heatmap - ReactomeAnalysisResult function",
      "topics": [
        "plot_gsva_heatmap,ReactomeAnalysisResult-method"
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      "page": "plot_gsva_pathway",
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      "concept": [
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      "topics": [
        "plot_gsva_pathway"
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      "page": "plot_gsva_pathway-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - plot_gsva_pathway",
      "topics": [
        "plot_gsva_pathway,ReactomeAnalysisResult-method"
      ]
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    {
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      "title": "plot_gsva_pca",
      "topics": [
        "plot_gsva_pca"
      ]
    },
    {
      "page": "plot_gsva_pca-ReactomeAnalysisResult-method",
      "title": "plot_gsva_pca - ReactomeAnalysisResult",
      "topics": [
        "plot_gsva_pca,ReactomeAnalysisResult-method"
      ]
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      "concept": [
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      "topics": [
        "plot_heatmap"
      ]
    },
    {
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      "title": "plot_heatmap - ReactomeAnalysisResult",
      "topics": [
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    },
    {
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      "title": "plot_volcano",
      "concept": [
        "ReactomeAnalysisResult functions"
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      "topics": [
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    },
    {
      "page": "plot_volcano-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - plot_volcano",
      "topics": [
        "plot_volcano,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "print-ReactomeAnalysisRequest-method",
      "title": "print - ReactomeAnalysisRequest",
      "topics": [
        "print,ReactomeAnalysisRequest-method"
      ]
    },
    {
      "page": "print-ReactomeAnalysisResult-method",
      "title": "print - ReactomeAnalysisResult",
      "topics": [
        "print,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "reactome_links",
      "title": "reactome_links",
      "concept": [
        "ReactomeAnalysisResult functions"
      ],
      "topics": [
        "reactome_links"
      ]
    },
    {
      "page": "reactome_links-ReactomeAnalysisResult-method",
      "title": "ReactomeAnalysisResult - reactome_links",
      "topics": [
        "reactome_links,ReactomeAnalysisResult-method"
      ]
    },
    {
      "page": "ReactomeAnalysisRequest",
      "title": "ReactomeAnalysisRequest class",
      "topics": [
        "ReactomeAnalysisRequest"
      ]
    },
    {
      "page": "ReactomeAnalysisResult-class",
      "title": "ReactomeAnalysisResult class",
      "topics": [
        "ReactomeAnalysisResult",
        "ReactomeAnalysisResult-class"
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    },
    {
      "page": "remove_dataset",
      "title": "remove_dataset",
      "topics": [
        "remove_dataset"
      ]
    },
    {
      "page": "remove_dataset-ReactomeAnalysisRequest-method",
      "title": "remove_dataset - ReactomeAnalysisRequest",
      "topics": [
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      "page": "result_types",
      "title": "result_types",
      "concept": [
        "ReactomeAnalysisResult functions"
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