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  "Type": "Package",
  "Title": "Creation and Analysis of Pathway Expression Profiles (PEPs)",
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  "Date": "2019-03-30",
  "Author": "Francesco Napolitano <franapoli@gmail.com>",
  "Maintainer": "Francesco Napolitano <franapoli@gmail.com>",
  "Description": "Pathway Expression Profiles (PEPs) are based on the\nexpression of pathways (defined as sets of genes) as opposed to\nindividual genes. This package converts gene expression\nprofiles to PEPs and performs enrichment analysis of both\npathways and experimental conditions, such as \"drug set\nenrichment analysis\" and \"gene2drug\" drug discovery analysis\nrespectively.",
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  "Repository": "https://bioc.r-universe.dev",
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    "buildPEPs",
    "CategorizedCollection",
    "checkRepository",
    "clearCache",
    "CondSEA",
    "createMergedRepository",
    "createRepository",
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    "getCollections",
    "getDetails",
    "getResults",
    "importFromRawMode",
    "importMSigDB.xml",
    "loadCollection",
    "loadESmatrix",
    "loadPVmatrix",
    "loadSampleGEP",
    "loadSamplePWS",
    "makeCollectionIDs",
    "openRepository",
    "PathSEA",
    "setId2setName"
  ],
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    {
      "page": "gep2pep-package",
      "title": "gep2pep: creation and analysis of Pathway Expression Profiles",
      "topics": [
        "gep2pep-package",
        "gep2pep"
      ]
    },
    {
      "page": "addSingleGeneSets",
      "title": "Adds a collection of single-gene psuedo-sets.",
      "topics": [
        "addSingleGeneSets"
      ]
    },
    {
      "page": "as.CategorizedCollection",
      "title": "Converts GeneSetCollection objects to CategorizedCollection objects.",
      "topics": [
        "as.CategorizedCollection"
      ]
    },
    {
      "page": "buildPEPs",
      "title": "Build PEPs from GEPs and stores them in the repository.",
      "topics": [
        "buildPEPs"
      ]
    },
    {
      "page": "CategorizedCollection",
      "title": "Constructor method for objects of class CategorizedCollection.",
      "topics": [
        "CategorizedCollection"
      ]
    },
    {
      "page": "CategorizedCollection-class",
      "title": "A class to contain categorized gene set collection",
      "topics": [
        "CategorizedCollection-class"
      ]
    },
    {
      "page": "checkRepository",
      "title": "Check an existyng repository for consistency",
      "topics": [
        "checkRepository"
      ]
    },
    {
      "page": "clearCache",
      "title": "Clear cached ranked matrices",
      "topics": [
        "clearCache"
      ]
    },
    {
      "page": "CondSEA",
      "title": "Performs Condition Set Enrichment Analysis",
      "topics": [
        "CondSEA"
      ]
    },
    {
      "page": "createMergedRepository",
      "title": "Merge multiple PEPs to build a repository of consensus PEPs",
      "topics": [
        "createMergedRepository"
      ]
    },
    {
      "page": "createRepository",
      "title": "Creates a repository of pathway collections.",
      "topics": [
        "createRepository"
      ]
    },
    {
      "page": "exportSEA",
      "title": "Export CondSEA or PathSEA results to XLS format",
      "topics": [
        "exportSEA"
      ]
    },
    {
      "page": "gene2pathways",
      "title": "Finds pathways including a given gene.",
      "topics": [
        "gene2pathways"
      ]
    },
    {
      "page": "getCollections",
      "title": "Returns the names of the pathway collections in a repository.",
      "topics": [
        "getCollections"
      ]
    },
    {
      "page": "getDetails",
      "title": "Extracts the details matrix from 'CondSEA' or 'PathSEA' output",
      "topics": [
        "getDetails"
      ]
    },
    {
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      "topics": [
        "getResults"
      ]
    },
    {
      "page": "importFromRawMode",
      "title": "Imports PEPs created in raw mode",
      "topics": [
        "importFromRawMode"
      ]
    },
    {
      "page": "importMSigDB.xml",
      "title": "Imports pathways data from an MSigDB XML file.",
      "topics": [
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      ]
    },
    {
      "page": "loadCollection",
      "title": "Loads a collection of pathways from the repository",
      "topics": [
        "loadCollection"
      ]
    },
    {
      "page": "loadESmatrix",
      "title": "Loads the matrix of Enrichment Scores for a collection",
      "topics": [
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      ]
    },
    {
      "page": "loadPVmatrix",
      "title": "Loads the matrix of p-values for a collection",
      "topics": [
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      ]
    },
    {
      "page": "loadSampleGEP",
      "title": "Loads sample Gene Expression Profiles",
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      ]
    },
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      ]
    },
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      ]
    },
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      ]
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      ]
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    {
      "page": "setId2setName",
      "title": "Converts gene set IDs to gene set names",
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      ]
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