{
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  "Package": "epigenomix",
  "Type": "Package",
  "Title": "Epigenetic and gene transcription data normalization and\nintegration with mixture models",
  "Version": "1.53.0",
  "Date": "2021-11-18",
  "Author": "Hans-Ulrich Klein, Martin Schaefer",
  "Maintainer": "Hans-Ulrich Klein <h.klein@uni-muenster.de>",
  "Description": "A package for the integrative analysis of RNA-seq or\nmicroarray based gene transcription and histone modification\ndata obtained by ChIP-seq. The package provides methods for\ndata preprocessing and matching as well as methods for fitting\nbayesian mixture models in order to detect genes with\ndifferences in both data types.",
  "License": "LGPL-3",
  "biocViews": "ChIPSeq, GeneExpression, DifferentialExpression,\nClassification",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:25 UTC",
  "RemoteUrl": "https://github.com/bioc/epigenomix",
  "RemoteRef": "HEAD",
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  "_published": "2026-05-30T12:05:44.517Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "weights"
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      "title": "Example gene expression data set.",
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      ],
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      "table": false,
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      "tojson": false
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      "class": [
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        "calculateCrossCorrelation,GRanges-method"
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    },
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        "ChIPseqSet,matrix,GRanges-method",
        "ChIPseqSet,matrix,GRangesList-method",
        "ChIPseqSet-class",
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        "cpm",
        "cpm,ChIPseqSet-method"
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    },
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      "page": "eSet",
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      "topics": [
        "eSet"
      ]
    },
    {
      "page": "fpkm",
      "title": "Example RNA-seq data set.",
      "topics": [
        "fpkm"
      ]
    },
    {
      "page": "getAlignmentQuality",
      "title": "Calculation of basic alignments statistics",
      "topics": [
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        "getAlignmentQuality,character-method"
      ]
    },
    {
      "page": "integrateData",
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      "topics": [
        "integrateData",
        "integrateData,ExpressionSet,ChIPseqSet,character,character-method",
        "integrateData,ExpressionSet,ChIPseqSet,character,missing-method",
        "integrateData,ExpressionSetIllumina,ChIPseqSet,character,character-method",
        "integrateData,ExpressionSetIllumina,ChIPseqSet,character,missing-method"
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    },
    {
      "page": "mappedReads",
      "title": "Mapped reads obtained from a anti-histone ChIP-seq experiment.",
      "topics": [
        "mappedReads"
      ]
    },
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      "topics": [
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        "matchProbeToPromoter,list,data.frame-method"
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    },
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      "topics": [
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        "classification",
        "classification,MixModel,character-method",
        "classification,MixModel,missing-method",
        "components",
        "components,MixModel-method",
        "dim,MixModel-method",
        "length,MixModel-method",
        "listClassificationMethods",
        "listClassificationMethods,MixModel-method",
        "MixModel-class",
        "mmData",
        "mmData,MixModel-method",
        "show,MixModel-method",
        "summary,MixModel-method",
        "summary,MixModelBayes-method",
        "weights,MixModel-method"
      ]
    },
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      "page": "MixModelBayes-class",
      "title": "Class '\"MixModelBayes\"'",
      "topics": [
        "acceptanceRate",
        "acceptanceRate,MixModelBayes-method",
        "chains",
        "chains,MixModelBayes-method",
        "MixModelBayes-class"
      ]
    },
    {
      "page": "MixModelML-class",
      "title": "Class '\"MixModelML\"'",
      "topics": [
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        "convergence,MixModelML-method",
        "MixModelML-class"
      ]
    },
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      "page": "MixtureComponent-class",
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      "topics": [
        "MixtureComponent-class",
        "show,MixtureComponent-method"
      ]
    },
    {
      "page": "mlMixModel",
      "title": "Fits a mixture model using the maximum likelihood principle.",
      "topics": [
        "mlMixModel",
        "mlMixModel,numeric-method"
      ]
    },
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      "page": "normalize",
      "title": "Normalization of ChIP-seq and other count data",
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        "normalize",
        "normalize,ChIPseqSet-method",
        "normalize,ExpressionSet-method"
      ]
    },
    {
      "page": "normalizeChIP",
      "title": "Normalization of ChIP-seq count data. (deprecated)",
      "topics": [
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        "normalizeChIP,ChIPseqSet,character-method"
      ]
    },
    {
      "page": "plotChains",
      "title": "Produces trace plots for a Bayesian mixture model",
      "topics": [
        "plotChains",
        "plotChains,MixModelBayes-method"
      ]
    },
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      "page": "plotClassification",
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        "plotClassification,MixModel-method"
      ]
    },
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      "page": "plotComponents",
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        "plotComponents,MixModel-method"
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        "summarizeReads,GRangesList,GRanges,character-method",
        "summarizeReads,GRangesList,GRanges,missing-method",
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