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  "Package": "Mergeomics",
  "Type": "Package",
  "Title": "Integrative network analysis of omics data",
  "Version": "1.41.0",
  "Date": "2016-01-04",
  "Author": "Ville-Petteri Makinen, Le Shu, Yuqi Zhao, Zeyneb Kurt, Bin\nZhang, Xia Yang",
  "Maintainer": "Zeyneb Kurt <zeynebkurt@gmail.com>",
  "Description": "The Mergeomics pipeline serves as a flexible framework for\nintegrating multidimensional omics-disease associations,\nfunctional genomics, canonical pathways and gene-gene\ninteraction networks to generate mechanistic hypotheses. It\nincludes two main parts, 1) Marker set enrichment analysis\n(MSEA); 2) Weighted Key Driver Analysis (wKDA).",
  "biocViews": "Software",
  "License": "GPL (>= 2)",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:38 UTC",
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    "kda2cytoscape",
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    "kda2cytoscape.colormap",
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    "MSEA.KDA.onestep",
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    "ssea.analyze.simulate",
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    {
      "page": "Mergeomics-package",
      "title": "Integrative network analysis of omics data",
      "topics": [
        "Mergeomics-package",
        "Mergeomics"
      ]
    },
    {
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      "title": "Key Driver Analyzing results",
      "topics": [
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    },
    {
      "page": "kda.analyze",
      "title": "Weighted key driver analysis (wKDA) main function",
      "topics": [
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      "title": "Calculate enrichment score for wKDA",
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      "title": "Organize and save results",
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      "title": "Trim numbers before save",
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      "title": "Prepare graph topology for weighted key driver analysis",
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      "title": "Extract overlapping co-hubs",
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    {
      "page": "kda.start.modules",
      "title": "Import module descriptions",
      "topics": [
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    },
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      "title": "Generate input files for Cytoscape",
      "topics": [
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      "title": "Trace module memberships of genes",
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      "title": "Assign one color to each unique module",
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      "title": "Select top key drivers for each module",
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      "title": "Generate input files for Himmeli",
      "topics": [
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      "title": "Trace module memberships of genes",
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    },
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      "title": "Marker set enrichment analysis (MSEA)",
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    },
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      "title": "Collect enrichment score statistics for MSEA",
      "topics": [
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    },
    {
      "page": "ssea.analyze.randgenes",
      "title": "Estimate enrichment from randomized genes",
      "topics": [
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      ]
    },
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      "page": "ssea.analyze.randloci",
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      "title": "Simulate scores for MSEA",
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      "title": "Organize and save MSEA results",
      "topics": [
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      "page": "ssea.finish.details",
      "title": "Organize and save module, gene, top locus, Ps of MSEA results",
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      "page": "ssea.finish.fdr",
      "title": "Organize and save FDR results of the MSEA",
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      "title": "Organize and save gene-realted MSEA results",
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      "page": "ssea.meta",
      "title": "Merge multiple MSEA results into meta MSEA",
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      "title": "Construct hierarchical representation of components",
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      "title": "Create a job for MSEA",
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      "title": "Check parameters before MSEA",
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      "page": "ssea2kda.analyze",
      "title": "Apply second MSEA after merging the modules",
      "topics": [
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    },
    {
      "page": "ssea2kda.import",
      "title": "Import genes and top markers from original files",
      "topics": [
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    },
    {
      "page": "tool.aggregate",
      "title": "Aggregate the entries",
      "topics": [
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    },
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      "title": "Hierarchical clustering of nodes",
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    },
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      "title": "Static hierarchical clustering",
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      "title": "Calculate overlaps between groups (main function)",
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    },
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      "page": "tool.coalesce.exec",
      "title": "Find, merge, and trim overlapping clusters",
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      "title": "Find overlapping clusters",
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      "title": "Merge overlapping clusters",
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      "title": "Estimate False Discovery Rates (FDR)",
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    },
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      "page": "tool.fdr.bh",
      "title": "Benjamini and Hochberg False Discovery Rate",
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    },
    {
      "page": "tool.fdr.empirical",
      "title": "Estimate Empirical False Discovery Rates",
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    },
    {
      "page": "tool.graph.degree",
      "title": "Find degrees of the nodes",
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    {
      "page": "tool.graph.list",
      "title": "Return edge list for each node",
      "topics": [
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    },
    {
      "page": "tool.metap",
      "title": "Estimate meta P-values",
      "topics": [
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    },
    {
      "page": "tool.normalize",
      "title": "Estimate statistical scores based on Gauss distribution",
      "topics": [
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    },
    {
      "page": "tool.normalize.quality",
      "title": "Check normalization quality",
      "topics": [
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      "page": "tool.overlap",
      "title": "Calculate overlaps between groups of specified items",
      "topics": [
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    },
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      "page": "tool.read",
      "title": "Read a data frame from a file",
      "topics": [
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    },
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      "page": "tool.save",
      "title": "Save a data frame in tab-delimited file",
      "topics": [
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    },
    {
      "page": "tool.subgraph",
      "title": "Determine network neighbors for a set of nodes",
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    },
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      "title": "Find edges to adjacent nodes",
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      "title": "Search neighborhoods for given nodes",
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    },
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      "page": "tool.subgraph.stats",
      "title": "Calculate node degrees and strengths",
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