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  "Title": "Generalized Reporter Score-Based Enrichment Analysis for Omics\nData",
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  "Description": "Inspired by the classic 'RSA', we developed the improved\n'Generalized Reporter Score-based Analysis (GRSA)' method,\nimplemented in the R package 'ReporterScore', along with\ncomprehensive visualization methods and pathway databases.\n'GRSA' is a threshold-free method that works well with all\ntypes of biomedical features, such as genes, chemical\ncompounds, and microbial species. Importantly, the 'GRSA'\nsupports multi-group and longitudinal experimental designs,\nbecause of the included multi-group-compatible statistical\nmethods.",
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  "BugReports": "https://github.com/Asa12138/ReporterScore/issues",
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  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://asa12138.r-universe.dev",
  "Date/Publication": "2026-04-28 08:50:35 UTC",
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    "name": "Chen Peng (彭)",
    "description": "PhD Student, Zhejiang University. Bioinformatics, Microbiome and Exposome."
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    "c_means",
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    "cm_test_k",
    "combine_rs_res",
    "custom_modulelist",
    "custom_modulelist_from_org",
    "download_org_pathway",
    "export_report_table",
    "extract_cluster",
    "gene2ko",
    "get_all_pathway_net_index",
    "get_features",
    "get_KOs",
    "get_org_pathway",
    "get_reporter_score",
    "GRSA",
    "GRSA_by_cm",
    "KO_enrich",
    "KO_fisher",
    "KO_gsa",
    "KO_gsea",
    "KO_gsva",
    "KO_padog",
    "KO_safe",
    "KO_sea",
    "ko.test",
    "load_CARDinfo",
    "load_CAZy_info",
    "load_Compound_htable",
    "load_CPDlist",
    "load_Enzyme_htable",
    "load_Enzyme_info",
    "load_GOinfo",
    "load_GOlist",
    "load_htable",
    "load_KO_desc",
    "load_KO_htable",
    "load_KOlist",
    "load_Module_htable",
    "load_org_pathway",
    "load_Pathway_htable",
    "load_pathway_xml_ls",
    "modify_description",
    "pathway_net_index",
    "plot_c_means",
    "plot_enrich_res",
    "plot_features_box",
    "plot_features_distribution",
    "plot_features_heatmap",
    "plot_features_in_pathway",
    "plot_features_network",
    "plot_htable",
    "plot_KEGG_map",
    "plot_KOs_box",
    "plot_KOs_distribution",
    "plot_KOs_heatmap",
    "plot_KOs_in_pathway",
    "plot_KOs_network",
    "plot_pathway_net",
    "plot_report",
    "plot_report_bar",
    "plot_report_circle_packing",
    "plot_significance",
    "pvalue2zs",
    "reporter_score",
    "RSA",
    "RSA_by_cm",
    "RSA_by_mg",
    "transform_modulelist",
    "up_level_KO",
    "update_CARDinfo",
    "update_CAZy_info",
    "update_Enzyme_info",
    "update_GOinfo",
    "update_GOlist",
    "update_htable",
    "update_KEGG",
    "update_KO_file",
    "update_org_pathway",
    "update_pathway_xml_ls"
  ],
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      "title": "Compound htable from 'KEGG'",
      "object": "Compound_htable",
      "file": "Compound_htable.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "compound1_name",
        "compound2_name",
        "compound3_name",
        "compound4_name",
        "Compound_id",
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      "table": true,
      "tojson": true
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      "file": "CPDlist.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "title": "human gene table",
      "object": "genedf",
      "file": "genedf.rda",
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      ],
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      "table": true,
      "tojson": true
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      ],
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      "tojson": true
    },
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      ],
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    },
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      "file": "mmu_kegg_pathway.rda",
      "class": [
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      ],
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        "tbl",
        "data.frame"
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        "module3_name",
        "Module_id",
        "Module_name"
      ],
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      "table": true,
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      "file": "Pathway_htable.rda",
      "class": [
        "data.frame"
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        "level2_name",
        "Pathway_id",
        "Pathway_name"
      ],
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      "table": true,
      "tojson": true
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      "object": "reporter_score_res",
      "file": "reporter_score_res.rda",
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      "name": "reporter_score_res2",
      "title": "'reporter_score()' result from KO_abundance_test",
      "object": "reporter_score_res",
      "file": "reporter_score_res.rda",
      "class": [
        "reporter_score"
      ],
      "fields": [],
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    {
      "page": "c_net_from_pathway_xml",
      "title": "Create a network from KEGG pathway XML files",
      "topics": [
        "c_net_from_pathway_xml"
      ]
    },
    {
      "page": "c_means",
      "title": "Test the proper clusters k for c_means",
      "concept": [
        "C_means"
      ],
      "topics": [
        "cm_test_k",
        "c_means"
      ]
    },
    {
      "page": "combine_rs_res",
      "title": "Combine the results of 'step by step GRSA'",
      "concept": [
        "GRSA"
      ],
      "topics": [
        "combine_rs_res"
      ]
    },
    {
      "page": "Compound_htable",
      "title": "Compound htable from 'KEGG'",
      "concept": [
        "data"
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      "topics": [
        "Compound_htable"
      ]
    },
    {
      "page": "CPDlist",
      "title": "The CPDlist used for enrichment.",
      "concept": [
        "data"
      ],
      "topics": [
        "CPDlist"
      ]
    },
    {
      "page": "custom_modulelist",
      "title": "Build a custom modulelist",
      "concept": [
        "modulelist"
      ],
      "topics": [
        "custom_modulelist",
        "transform_modulelist"
      ]
    },
    {
      "page": "custom_modulelist_from_org",
      "title": "Custom modulelist from a specific organism",
      "concept": [
        "modulelist"
      ],
      "topics": [
        "custom_modulelist_from_org"
      ]
    },
    {
      "page": "export_report_table",
      "title": "Export report score result tables",
      "topics": [
        "export_report_table"
      ]
    },
    {
      "page": "gene2ko",
      "title": "Transfer gene symbol table to KO table",
      "topics": [
        "gene2ko"
      ]
    },
    {
      "page": "genedf",
      "title": "human gene table",
      "concept": [
        "test_data"
      ],
      "topics": [
        "genedf"
      ]
    },
    {
      "page": "get_all_pathway_net_index",
      "title": "Create an index for all KEGG pathway networks",
      "topics": [
        "get_all_pathway_net_index"
      ]
    },
    {
      "page": "get_features",
      "title": "get features in a modulelist",
      "concept": [
        "modulelist"
      ],
      "topics": [
        "get_features",
        "get_KOs"
      ]
    },
    {
      "page": "get_reporter_score",
      "title": "Calculate reporter score",
      "concept": [
        "GRSA"
      ],
      "topics": [
        "get_reporter_score"
      ]
    },
    {
      "page": "GOlist",
      "title": "The GOlist used for enrichment.",
      "concept": [
        "data"
      ],
      "topics": [
        "GOlist"
      ]
    },
    {
      "page": "hsa_kegg_pathway",
      "title": "pathway information for \"hsa\"",
      "concept": [
        "data"
      ],
      "topics": [
        "hsa_kegg_pathway"
      ]
    },
    {
      "page": "KO_abundance",
      "title": "The KOs abundance table and group table.",
      "concept": [
        "test_data"
      ],
      "topics": [
        "KO_abundance",
        "metadata"
      ]
    },
    {
      "page": "KO_enrich",
      "title": "Perform enrichment analysis",
      "concept": [
        "common_enrich"
      ],
      "topics": [
        "as.enrich_res",
        "KO_enrich"
      ]
    },
    {
      "page": "KO_fisher",
      "title": "Perform fisher's exact enrichment analysis",
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      "page": "KO_gsa",
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    },
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      "page": "KO_gsea",
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    },
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      "page": "KO_gsva",
      "title": "Perform Gene Set Variation Analysis",
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    },
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      "page": "KO_htable",
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      "topics": [
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    },
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      "page": "KO_padog",
      "title": "Perform Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)",
      "concept": [
        "common_enrich"
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    },
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      "page": "KO_safe",
      "title": "Perform Significance Analysis of Function and Expression",
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    },
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      "page": "KO_sea",
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    },
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      "page": "ko.test",
      "title": "Differential analysis or Correlation analysis for KO-abundance table",
      "concept": [
        "GRSA"
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    },
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      "page": "KOlist",
      "title": "The KOlist used for enrichment.",
      "concept": [
        "data"
      ],
      "topics": [
        "KOlist"
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    },
    {
      "page": "load_CARDinfo",
      "title": "Load the CARDinfo (from CARD database)",
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    },
    {
      "page": "load_CAZy_info",
      "title": "Load the CAZy_info (from CAZy database)",
      "topics": [
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    },
    {
      "page": "load_Enzyme_info",
      "title": "Load the Enzyme_info (from ExPASy Enzyme database)",
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    },
    {
      "page": "load_GOlist",
      "title": "Load the GOlist (from 'GO' database)",
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        "load_GOlist"
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    },
    {
      "page": "load_htable",
      "title": "Load the specific table (from 'KEGG')",
      "topics": [
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        "load_CPDlist",
        "load_Enzyme_htable",
        "load_htable",
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      "page": "load_pathway_xml_ls",
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      "topics": [
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      "concept": [
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      "topics": [
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    {
      "page": "modify_description",
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      "page": "Module_htable",
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      "topics": [
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      "title": "Plot enrich_res",
      "concept": [
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    },
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      "title": "Plot features boxplot",
      "topics": [
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    },
    {
      "page": "plot_features_distribution",
      "title": "plot the Z-score of features distribution",
      "topics": [
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    },
    {
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      "topics": [
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    },
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      "page": "plot_features_in_pathway",
      "title": "Plot features trend in one pathway or module",
      "topics": [
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    {
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      "title": "Plot features network",
      "topics": [
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        "plot_KOs_network"
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    },
    {
      "page": "plot_htable",
      "title": "Plot htable levels",
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    },
    {
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      "title": "plot_KEGG_map",
      "topics": [
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    },
    {
      "page": "plot_pathway_net",
      "title": "Plot a KEGG pathway network",
      "topics": [
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    {
      "page": "plot_report",
      "title": "Plot the reporter_res",
      "topics": [
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    },
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      "page": "plot_report_circle_packing",
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    {
      "page": "plot_significance",
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      "title": "Print rs_by_mg",
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    {
      "page": "pvalue2zs",
      "title": "Transfer p-value of KOs to Z-score",
      "concept": [
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      "concept": [
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      "title": "`reporter_score()` result from KO_abundance_test",
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      "topics": [
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        "reporter_score_res2"
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      "concept": [
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      "topics": [
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      "title": "ReporterScore",
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      "headings": [
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      "created": "2023-06-21 08:42:12",
      "modified": "2024-03-20 17:26:41",
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