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  "Date": "2024-12-16",
  "Title": "Differential Analysis of Hi-C Data",
  "Author": "Aaron Lun, Gordon Smyth",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>,\nGordon Smyth <smyth@wehi.edu.au>, Hannah Coughlin\n<coughlin.h@wehi.edu.au>",
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    "readMTX2IntSet",
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      "title": "Annotate bin pairs",
      "topics": [
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      "page": "boxPairs",
      "title": "Put bin pairs into boxes",
      "topics": [
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      ]
    },
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      "title": "Cluster bin pairs",
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      "title": "Identify genomic compartments",
      "topics": [
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      "title": "Count connecting read pairs",
      "topics": [
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      ]
    },
    {
      "page": "consolidatePairs",
      "title": "Consolidate results for interactions",
      "topics": [
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      ]
    },
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      "title": "Iterative correction of Hi-C counts",
      "topics": [
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      ]
    },
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      "title": "Cut up the genome",
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      ]
    },
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      "page": "diClusters",
      "title": "Cluster significant bin pairs to DIs",
      "topics": [
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    },
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      "title": "View diffHic user's guide",
      "topics": [
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        "diffHicUsersGuide"
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    },
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      "page": "DNaseHiC",
      "title": "Methods for processing DNase Hi-C data",
      "topics": [
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        "prepPseudoPairs",
        "segmentGenome"
      ]
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    {
      "page": "domainDirections",
      "title": "Calculate domain directionality",
      "topics": [
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      "title": "Collect local enrichment statistics for bin pairs",
      "topics": [
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      "title": "Extract a patch of the interaction space",
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    {
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      "topics": [
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      "title": "Filtering strategies for bin pairs",
      "topics": [
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        "filterTrended"
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      "title": "Filter bin pairs for likely peaks",
      "topics": [
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    },
    {
      "page": "getArea",
      "title": "Get interaction area",
      "topics": [
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      ]
    },
    {
      "page": "getPairData",
      "title": "Get read pair data",
      "topics": [
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    },
    {
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      "title": "Load data from an index file",
      "topics": [
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        "loadData"
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      "title": "Collect marginal counts for each bin",
      "topics": [
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