{
  "_id": "6a49754c424221e3da02e94c",
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  "Version": "1.23.0",
  "Date": "2026-03-05",
  "Title": "Clustering Algorithms for Bioconductor",
  "Description": "Wraps common clustering algorithms in an easily extended\nS4 framework. Backends are implemented for hierarchical,\nk-means and graph-based clustering. Several utilities are also\nprovided to compare and evaluate clustering results.",
  "Authors@R": "c(\nperson(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Stephanie\", \"Hicks\", role=\"ctb\"),\nperson(\"Basil\", \"Courbayre\", role=\"ctb\"),\nperson(\"Tuomas\", \"Borman\", role=\"ctb\"),\nperson(\"Leo\", \"Lahti\", role=\"ctb\")\n)",
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  "Collate": "AllClasses.R AllGenerics.R AgnesParam.R approxSilhouette.R\nbluster-package.R DbscanParam.R DianaParam.R AffinityParam.R\nBlusterParam.R bootstrapStability.R ClaraParam.R clusterRMSD.R\nclusterSweep.R compareClusterings.R DmmParam.R\nFixedNumberParam.R HclustParam.R HierarchicalParam.R\nKmeansParam.R linkClusters.R makeSNNGraph.R MbkmeansParam.R\nmergeCommunities.R neighborPurity.R nestedClusters.R\nNNGraphParam.R pairwiseModularity.R pairwiseRand.R PamParam.R\nRcppExports.R SomParam.R TwoStepParam.R utils.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:10 UTC",
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  "Author": "Aaron Lun [aut, cre],\nStephanie Hicks [ctb],\nBasil Courbayre [ctb],\nTuomas Borman [ctb],\nLeo Lahti [ctb]",
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    "neighborsToSNNGraph",
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    "NNGraphParam",
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    "PamParam",
    "show",
    "SNNGraphParam",
    "SomParam",
    "TwoStepParam",
    "updateObject"
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      "topics": [
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        ".extractScalarArguments",
        ".showScalarArguments"
      ]
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    {
      "page": "AffinityParam-class",
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        "AffinityParam-class",
        "clusterRows,ANY,AffinityParam-method",
        "show,AffinityParam-method"
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        "AgnesParam",
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        "show,AgnesParam-method"
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    {
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    {
      "page": "BlusterParam-class",
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        "show,BlusterParam-method",
        "[[,BlusterParam-method",
        "[[<-,BlusterParam-method"
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    {
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      ]
    },
    {
      "page": "ClaraParam-class",
      "title": "Clustering Large Applications",
      "topics": [
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        "ClaraParam",
        "ClaraParam-class",
        "clusterRows,ANY,ClaraParam-method",
        "show,ClaraParam-method"
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    {
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      "title": "Compute the RMSD per cluster",
      "topics": [
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      ]
    },
    {
      "page": "clusterRows",
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      "topics": [
        "clusterRows"
      ]
    },
    {
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      "title": "Clustering parameter sweeps",
      "topics": [
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    {
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      "title": "Compare pairs of clusterings",
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        "DbscanParam",
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        "DianaParam",
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      "title": "Dirichlet multinomial mixture clustering",
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        "DmmParam",
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        "show,DmmParam-method"
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    {
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      "title": "The FixedNumberParam class",
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        "centers,FixedNumberParam-method",
        "centers<-",
        "centers<-,FixedNumberParam-method",
        "FixedNumberParam-class",
        "show,FixedNumberParam-method"
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        "clusterRows,ANY,HclustParam-method",
        "HclustParam",
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        "show,KmeansParam-method",
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        "MbkmeansParam",
        "MbkmeansParam-class",
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      "title": "Merge communities from graph-based clustering",
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      "page": "neighborPurity",
      "title": "Compute neighborhood purity",
      "topics": [
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    {
      "page": "nestedClusters",
      "title": "Map nested clusterings",
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      "title": "Compute pairwise modularity",
      "topics": [
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    },
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      "page": "pairwiseRand",
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      "topics": [
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        "clusterRows,ANY,PamParam-method",
        "PamParam",
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      "title": "Clustering with self-organizing maps",
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        "show,SomParam-method",
        "SomParam",
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      "page": "TwoStepParam-class",
      "title": "Two step clustering with vector quantization",
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        "show,TwoStepParam-method",
        "TwoStepParam",
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      "title": "Flexible clustering for Bioconductor",
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      "headings": [
        "Introduction",
        "Based on distance matrices",
        "Hierarchical clustering",
        "Affinity propagation",
        "With a fixed number of clusters",
        "$k$-means clustering",
        "Self-organizing maps",
        "Graph-based clustering",
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        "Two-phase clustering",
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