{
  "_id": "6a212a91cd65a98ecbd22ae7",
  "Package": "fgsea",
  "Title": "Fast Gene Set Enrichment Analysis",
  "Version": "1.39.0",
  "Authors@R": "c(person(\"Gennady\", \"Korotkevich\", role = \"aut\"),\nperson(\"Vladimir\", \"Sukhov\", role = \"aut\"),\nperson(\"Nikita\", \"Golikov\", role = \"aut\"),\nperson(\"Nikolay\", \"Budin\", role = \"ctb\"),\nperson(\"Nikita\", \"Gusak\", role = \"ctb\"),\nperson(\"Zieman\", \"Mark\", role = \"ctb\"),\nperson(\"Alexey\", \"Sergushichev\", email = \"alsergbox@gmail.com\", role = c(\"aut\", \"cre\")))",
  "Description": "The package implements an algorithm for fast gene set\nenrichment analysis. Using the fast algorithm allows to make\nmore permutations and get more fine grained p-values, which\nallows to use accurate stantard approaches to multiple\nhypothesis correction.",
  "biocViews": "GeneExpression, DifferentialExpression, GeneSetEnrichment,\nPathways",
  "License": "MIT + file LICENCE",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/alserglab/fgsea/",
  "BugReports": "https://github.com/alserglab/fgsea/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:45 UTC",
  "RemoteUrl": "https://github.com/bioc/fgsea",
  "RemoteRef": "HEAD",
  "RemoteSha": "814dad48f0e2112bddac4087953abe6026ebcd76",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-04 07:19:08 UTC",
    "User": "root"
  },
  "Author": "Gennady Korotkevich [aut],\nVladimir Sukhov [aut],\nNikita Golikov [aut],\nNikolay Budin [ctb],\nNikita Gusak [ctb],\nZieman Mark [ctb],\nAlexey Sergushichev [aut, cre]",
  "Maintainer": "Alexey Sergushichev <alsergbox@gmail.com>",
  "MD5sum": "4cd3437f78c4458acfe6311c715f9850",
  "_user": "bioc",
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  "_created": "2026-06-04T07:19:08.000Z",
  "_published": "2026-06-04T07:34:41.185Z",
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  "_homeurl": "https://github.com/alserglab/fgsea",
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  "_exports": [
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    "collapsePathways",
    "collapsePathwaysORA",
    "fgsea",
    "fgseaLabel",
    "fgseaMultilevel",
    "fgseaSimple",
    "fora",
    "geseca",
    "gesecaSimple",
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    "mapIdsList",
    "multilevelError",
    "plotCoregulationProfile",
    "plotCoregulationProfileImage",
    "plotCoregulationProfileReduction",
    "plotCoregulationProfileSpatial",
    "plotEnrichment",
    "plotEnrichmentData",
    "plotGesecaTable",
    "plotGseaTable",
    "reactomePathways",
    "writeGmtPathways"
  ],
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      "name": "exampleExpressionMatrix",
      "title": "Example of expression values obtained for GSE14308.",
      "object": "exampleExpressionMatrix",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "GSM357839",
        "GSM357841",
        "GSM357842",
        "GSM357843",
        "GSM357844",
        "GSM357845",
        "GSM357847",
        "GSM357848",
        "GSM357849",
        "GSM357850",
        "GSM357852",
        "GSM357853"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Example list of mouse Reactome pathways.",
      "object": "examplePathways",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "title": "Example vector of gene-level statistics obtained for Th1 polarization.",
      "object": "exampleRanks",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
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  "_help": [
    {
      "page": "calcGseaStat",
      "title": "Calculates GSEA statistics for a given query gene set",
      "topics": [
        "calcGseaStat"
      ]
    },
    {
      "page": "calcGseaStatBatchCpp",
      "title": "Calculates GSEA statistic valus for all gene sets in `selectedStats` list.",
      "topics": [
        "calcGseaStatBatchCpp"
      ]
    },
    {
      "page": "collapsePathways",
      "title": "Collapse list of enriched pathways to independent ones.",
      "topics": [
        "collapsePathways"
      ]
    },
    {
      "page": "collapsePathwaysGeseca",
      "title": "Collapse list of enriched pathways to independent ones (GESECA version, highly experimental).",
      "topics": [
        "collapsePathwaysGeseca"
      ]
    },
    {
      "page": "collapsePathwaysORA",
      "title": "Collapse list of enriched pathways to independent ones. Version for ORA hypergeometric test.",
      "topics": [
        "collapsePathwaysORA"
      ]
    },
    {
      "page": "exampleExpressionMatrix",
      "title": "Example of expression values obtained for GSE14308.",
      "topics": [
        "exampleExpressionMatrix"
      ]
    },
    {
      "page": "examplePathways",
      "title": "Example list of mouse Reactome pathways.",
      "topics": [
        "examplePathways"
      ]
    },
    {
      "page": "exampleRanks",
      "title": "Example vector of gene-level statistics obtained for Th1 polarization.",
      "topics": [
        "exampleRanks"
      ]
    },
    {
      "page": "fgsea",
      "title": "Wrapper to run methods for preranked gene set enrichment analysis.",
      "topics": [
        "fgsea"
      ]
    },
    {
      "page": "fgseaLabel",
      "title": "Runs label-permuring gene set enrichment analysis.",
      "topics": [
        "fgseaLabel"
      ]
    },
    {
      "page": "fgseaMultilevel",
      "title": "Runs preranked gene set enrichment analysis.",
      "topics": [
        "fgseaMultilevel"
      ]
    },
    {
      "page": "fgseaSimple",
      "title": "Runs preranked gene set enrichment analysis.",
      "topics": [
        "fgseaSimple"
      ]
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      "page": "fgseaSimpleImpl",
      "title": "Runs preranked gene set enrichment analysis for preprocessed input data.",
      "topics": [
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      "title": "Simple overrepresentation analysis based on hypergeometric test",
      "topics": [
        "fora"
      ]
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    {
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      "title": "Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis",
      "topics": [
        "geseca"
      ]
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      "topics": [
        "gesecaSimple"
      ]
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    {
      "page": "gmtPathways",
      "title": "Returns a list of pathways from a GMT file.",
      "topics": [
        "gmtPathways"
      ]
    },
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      "page": "mapIdsList",
      "title": "Effeciently converts collection of pathways using AnnotationDbi::mapIds function. Parameters are the sames as for mapIds except for keys, which is assumed to be a list of vectors.",
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        "mapIdsList"
      ]
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      "page": "multilevelError",
      "title": "Calculates the expected error for the standard deviation of the P-value logarithm.",
      "topics": [
        "multilevelError"
      ]
    },
    {
      "page": "multilevelImpl",
      "title": "Calculates P-values for preprocessed data.",
      "topics": [
        "multilevelImpl"
      ]
    },
    {
      "page": "plotCoregulationProfile",
      "title": "Plots expression profile of a gene set",
      "topics": [
        "plotCoregulationProfile"
      ]
    },
    {
      "page": "plotCoregulationProfileImage",
      "title": "Spatial visualization of GESECA scores for individual cells",
      "topics": [
        "plotCoregulationProfileImage"
      ]
    },
    {
      "page": "plotCoregulationProfileReduction",
      "title": "Plot a spatial expression profile of a gene set",
      "topics": [
        "plotCoregulationProfileReduction"
      ]
    },
    {
      "page": "plotCoregulationProfileSpatial",
      "title": "Plot a spatial expression profile of a gene set",
      "topics": [
        "plotCoregulationProfileSpatial"
      ]
    },
    {
      "page": "plotEnrichment",
      "title": "Plots GSEA enrichment plot. For more flexibility use `plotEnrichmentData` function.",
      "topics": [
        "plotEnrichment"
      ]
    },
    {
      "page": "plotEnrichmentData",
      "title": "Returns data required for doing an enrichment plot.",
      "topics": [
        "plotEnrichmentData"
      ]
    },
    {
      "page": "plotGesecaTable",
      "title": "Plots table of gene set profiles.",
      "topics": [
        "plotGesecaTable"
      ]
    },
    {
      "page": "plotGseaTable",
      "title": "Plots table of enrichment graphs using ggplot and gridExtra.",
      "topics": [
        "plotGseaTable"
      ]
    },
    {
      "page": "reactomePathways",
      "title": "Returns a list of Reactome pathways for given Entrez gene IDs",
      "topics": [
        "reactomePathways"
      ]
    },
    {
      "page": "writeGmtPathways",
      "title": "Write collection of pathways (list of vectors) to a gmt file",
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      ]
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