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  "Package": "apcluster",
  "Type": "Package",
  "Title": "Affinity Propagation Clustering",
  "Version": "1.4.14",
  "Date": "2025-09-09",
  "Authors@R": "c(person(given = \"Ulrich\",\nfamily = \"Bodenhofer\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ulrich@bodenhofer.com\"),\nperson(given = \"Johannes\",\nfamily = \"Palme\",\nrole = \"ctb\"),\nperson(given = \"Chrats\",\nfamily = \"Melkonian\",\nrole = \"ctb\"),\nperson(given = \"Andreas\",\nfamily = \"Kothmeier\",\nrole = \"aut\"),\nperson(given = \"Nikola\",\nfamily = \"Kostic\",\nrole = \"ctb\"))",
  "Maintainer": "Ulrich Bodenhofer <ulrich@bodenhofer.com>",
  "Description": "Implements Affinity Propagation clustering introduced by\nFrey and Dueck (2007) <DOI:10.1126/science.1136800>. The\nalgorithms are largely analogous to the 'Matlab' code published\nby Frey and Dueck. The package further provides leveraged\naffinity propagation and an algorithm for exemplar-based\nagglomerative clustering that can also be used to join clusters\nobtained from affinity propagation. Various plotting functions\nare available for analyzing clustering results.",
  "License": "GPL (>= 2)",
  "Collate": "AllClasses.R AllGenerics.R access-methods.R coerce-methods.R\nshow-methods.R labels-methods.R length-methods.R revDend.R\nheatmap-methods.R plot-methods.R cutree-methods.R\nsort-methods.R aggExCluster-methods.R apcluster-methods.R\napclusterL-methods.R apclusterK-methods.R apclusterDemo.R\npreferenceRange-methods.R similarity.R simpleDist.R\nconversions.R",
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  "Repository": "https://ubod.r-universe.dev",
  "Date/Publication": "2025-09-09 10:58:50 UTC",
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  "Author": "Ulrich Bodenhofer [aut, cre],\nJohannes Palme [ctb],\nChrats Melkonian [ctb],\nAndreas Kothmeier [aut],\nNikola Kostic [ctb]",
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    "apcluster",
    "apclusterDemo",
    "apclusterK",
    "apclusterL",
    "as.dendrogram",
    "as.DenseSimilarityMatrix",
    "as.hclust",
    "as.SparseSimilarityMatrix",
    "corSimMat",
    "cutree",
    "expSimMat",
    "heatmap",
    "labels",
    "linKernel",
    "linSimMat",
    "negDistMat",
    "plot",
    "preferenceRange",
    "show",
    "similarity"
  ],
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    {
      "page": "apcluster-package",
      "title": "APCluster Package",
      "topics": [
        "apcluster-package"
      ]
    },
    {
      "page": "aggExCluster-methods",
      "title": "Exemplar-based Agglomerative Clustering",
      "topics": [
        "aggExCluster",
        "aggexcluster",
        "aggExCluster,character,ANY-method",
        "aggExCluster,function,ANY-method",
        "aggExCluster,Matrix,ExClust-method",
        "aggExCluster,matrix,ExClust-method",
        "aggExCluster,Matrix,missing-method",
        "aggExCluster,matrix,missing-method",
        "aggExCluster,missing,ExClust-method",
        "aggExCluster-methods"
      ]
    },
    {
      "page": "AggExResult-class",
      "title": "Class \"AggExResult\"",
      "topics": [
        "AggExResult",
        "aggexresult",
        "AggExResult-class",
        "length,AggExResult-method",
        "similarity,AggExResult-method",
        "[,AggExResult,index,missing,missing-method",
        "[[,AggExResult,index,missing-method"
      ]
    },
    {
      "page": "apcluster-methods",
      "title": "Affinity Propagation",
      "topics": [
        "apcluster",
        "apcluster,character,ANY-method",
        "apcluster,dgTMatrix,missing-method",
        "apcluster,function,ANY-method",
        "apcluster,Matrix,missing-method",
        "apcluster,matrix,missing-method",
        "apcluster,sparseMatrix,missing-method",
        "apcluster-methods"
      ]
    },
    {
      "page": "apclusterDemo",
      "title": "Affinity Propagation Demo",
      "topics": [
        "apclusterDemo"
      ]
    },
    {
      "page": "apclusterK-methods",
      "title": "Affinity Propagation for Pre-defined Number of Clusters",
      "topics": [
        "apclusterK",
        "apclusterK,character,ANY-method",
        "apclusterK,dgTMatrix,missing-method",
        "apclusterK,function,ANY-method",
        "apclusterK,Matrix,missing-method",
        "apclusterK,matrix,missing-method",
        "apclusterK,sparseMatrix,missing-method",
        "apclusterK-methods"
      ]
    },
    {
      "page": "apclusterL-methods",
      "title": "Leveraged Affinity Propagation",
      "topics": [
        "apclusterL",
        "apclusterL,character,ANY-method",
        "apclusterL,function,ANY-method",
        "apclusterL,matrix,missing-method",
        "apclusterL-methods"
      ]
    },
    {
      "page": "APResult-class",
      "title": "Class \"APResult\"",
      "topics": [
        "APResult",
        "apresult",
        "APResult-class",
        "length,APResult-method",
        "similarity",
        "similarity,APResult-method",
        "[,APResult,index,missing,missing-method",
        "[[,APResult,index,missing-method"
      ]
    },
    {
      "page": "coerce-methods",
      "title": "Coercion of cluster hierarchies",
      "topics": [
        "as.dendrogram",
        "as.dendrogram,AggExResult-method",
        "as.dendrogram,ExClust-method",
        "as.hclust",
        "as.hclust,AggExResult-method",
        "as.hclust,ExClust-method"
      ]
    },
    {
      "page": "conversions",
      "title": "Conversions Between Dense and Sparse Similarity Matrices",
      "topics": [
        "as.DenseSimilarityMatrix",
        "as.DenseSimilarityMatrix,Matrix-method",
        "as.DenseSimilarityMatrix,matrix-method",
        "as.DenseSimilarityMatrix,sparseMatrix-method",
        "as.DenseSimilarityMatrix-method",
        "as.SparseSimilarityMatrix",
        "as.SparseSimilarityMatrix,Matrix-method",
        "as.SparseSimilarityMatrix,matrix-method",
        "as.SparseSimilarityMatrix,sparseMatrix-method",
        "as.SparseSimilarityMatrix-methods",
        "conversions"
      ]
    },
    {
      "page": "cutree-methods",
      "title": "Cut Out Clustering Level from Cluster Hierarchy",
      "topics": [
        "cutree",
        "cutree,AggExResult-method",
        "cutree,APResult-method",
        "cutree-methods"
      ]
    },
    {
      "page": "ExClust-class",
      "title": "Class \"ExClust\"",
      "topics": [
        "ExClust",
        "exclust",
        "ExClust-class",
        "length,ExClust-method",
        "similarity,ExClust-method",
        "[,ExClust,index,missing,missing-method",
        "[[,ExClust,index,missing-method"
      ]
    },
    {
      "page": "heatmap-methods",
      "title": "Plot Heatmap",
      "topics": [
        "heatmap",
        "heatmap,AggExResult,matrix-method",
        "heatmap,AggExResult,missing-method",
        "heatmap,ExClust,Matrix-method",
        "heatmap,ExClust,matrix-method",
        "heatmap,ExClust,missing-method",
        "heatmap,ExClust,sparseMatrix-method",
        "heatmap,matrix,missing-method",
        "heatmap,missing,matrix-method",
        "heatmap-methods"
      ]
    },
    {
      "page": "labels-methods",
      "title": "Generate label vector from clustering result",
      "topics": [
        "labels",
        "labels,APResult-method",
        "labels,ExClust-method",
        "labels-methods"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plot Clustering Results",
      "topics": [
        "plot",
        "plot,AggExResult,data.frame-method",
        "plot,AggExResult,matrix-method",
        "plot,AggExResult,missing-method",
        "plot,APResult,missing-method",
        "plot,ExClust,data.frame-method",
        "plot,ExClust,matrix-method",
        "plot,ExClust,missing-method",
        "plot-methods"
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    {
      "page": "preferenceRange-methods",
      "title": "Determine Meaningful Ranges for Input Preferences",
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        "preferenceRange,dgTMatrix-method",
        "preferenceRange,Matrix-method",
        "preferenceRange,matrix-method",
        "preferenceRange,sparseMatrix-method",
        "preferenceRange-methods"
      ]
    },
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        "show,AggExResult-method",
        "show,APResult-method",
        "show,ExClust-method",
        "show-methods"
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    },
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        "expSimMat",
        "linKernel",
        "linSimMat",
        "negDistMat",
        "similarities"
      ]
    },
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        "sort,APResult-method",
        "sort,ExClust-method",
        "sort-methods"
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      "headings": [
        "Introduction",
        "Installation",
        "Getting Started",
        "Adjusting Input Preferences",
        "Exemplar-based Agglomerative Clustering",
        "Leveraged Affinity Propagation",
        "Sparse Affinity Propagation",
        "Processing Biological Sequences",
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