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  "Package": "HiContacts",
  "Title": "Analysing cool files in R with HiContacts",
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  "URL": "https://github.com/js2264/HiContacts",
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    "aggregate",
    "autocorrelate",
    "bbrColors",
    "bgrColors",
    "boost",
    "bwrColors",
    "cisTransRatio",
    "coarsen",
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    "contacts_yeast",
    "contacts_yeast_eco1",
    "coolerColors",
    "coverage",
    "despeckle",
    "detrend",
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    "divide",
    "getBorders",
    "getCompartments",
    "getDiamondInsulation",
    "getLoops",
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    "merge",
    "montage",
    "normalize",
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    "plotMatrix",
    "plotPs",
    "plotPsSlope",
    "plotSaddle",
    "plotScalogram",
    "rainbowColors",
    "scalogram",
    "subsample",
    "virtual4C"
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    {
      "page": "arithmetics",
      "title": "HiContacts arithmetics functionalities",
      "topics": [
        "aggregate,HiCExperiment-method",
        "arithmetics",
        "autocorrelate",
        "boost",
        "coarsen",
        "despeckle",
        "detrend",
        "divide",
        "merge,HiCExperiment,HiCExperiment-method",
        "normalize,HiCExperiment-method",
        "subsample"
      ]
    },
    {
      "page": "cisTransRatio",
      "title": "cisTransRatio",
      "topics": [
        "cisTransRatio"
      ]
    },
    {
      "page": "Contacts",
      "title": "Contacts",
      "topics": [
        "Contacts"
      ]
    },
    {
      "page": "Ps",
      "title": "Compute the law of distance-dependent contact frequency, a.k.a. P(s)",
      "topics": [
        "distanceLaw",
        "distanceLaw,GInteractions,missing-method",
        "distanceLaw,HiCExperiment,GRanges-method",
        "distanceLaw,HiCExperiment,missing-method",
        "distanceLaw,PairsFile,GRanges-method",
        "distanceLaw,PairsFile,missing-method",
        "localDistanceLaw",
        "Ps"
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      "title": "Contact map compartments",
      "topics": [
        "getCompartments"
      ]
    },
    {
      "page": "getDiamondInsulation",
      "title": "Contact map insulation",
      "topics": [
        "getBorders",
        "getDiamondInsulation"
      ]
    },
    {
      "page": "getLoops",
      "title": "Finding loops in contact map",
      "topics": [
        "getLoops"
      ]
    },
    {
      "page": "HiContacts-plots",
      "title": "HiContacts plotting functionalities",
      "topics": [
        "HiContacts-plots"
      ]
    },
    {
      "page": "palettes",
      "title": "Matrix palettes",
      "topics": [
        "afmhotrColors",
        "bbrColors",
        "bgrColors",
        "bwrColors",
        "coolerColors",
        "palettes",
        "rainbowColors"
      ]
    },
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      "title": "Plotting virtual 4C profiles",
      "topics": [
        "plot4C"
      ]
    },
    {
      "page": "plotMatrix",
      "title": "Plotting a contact matrix",
      "topics": [
        "montage",
        "montage,AggrHiCExperiment-method",
        "plotMatrix",
        "plotMatrix,AggrHiCExperiment-method",
        "plotMatrix,GInteractions-method",
        "plotMatrix,HiCExperiment-method",
        "plotMatrix,matrix-method"
      ]
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        "plotPsSlope"
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        "tracks"
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