{
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  "Package": "HiCDOC",
  "Title": "A/B compartment detection and differential analysis",
  "Version": "1.14.0",
  "Date": "2025-07-22",
  "Authors@R": "c(\nperson(\"Kurylo\", \"Cyril\", email = \"cyril.kurylo@inrae.fr\", role = c(\"aut\")),\nperson(\"Zytnicki\", \"Matthias\", email = \"matthias.zytnicki@inrae.fr\", role = c(\"aut\")),\nperson(\"Foissac\", \"Sylvain\", email = \"sylvain.foissac@inrae.fr\", role = c(\"aut\")),\nperson(\"Maigné\", \"Élise\", email = \"elise.maigne@inrae.fr\", role = c(\"aut\", \"cre\")))",
  "Description": "HiCDOC normalizes intrachromosomal Hi-C matrices, uses\nunsupervised learning to predict A/B compartments from multiple\nreplicates, and detects significant compartment changes between\nexperiment conditions. It provides a collection of functions\nassembled into a pipeline to filter and normalize the data,\npredict the compartments and visualize the results. It accepts\nseveral type of data: tabular `.tsv` files, Cooler `.cool` or\n`.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and\n`.bed` files.",
  "License": "LGPL-3",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:38 UTC",
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  "Author": "Kurylo Cyril [aut],\nZytnicki Matthias [aut],\nFoissac Sylvain [aut],\nMaigné Élise [aut, cre]",
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    "filterSmallChromosomes",
    "filterSparseReplicates",
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    "normalizeTechnicalBiases",
    "parameters",
    "parameters<-",
    "plotCentroids",
    "plotCompartmentChanges",
    "plotCompartments",
    "plotConcordanceDifferences",
    "plotConcordances",
    "plotDistanceEffect",
    "plotInteractions",
    "plotSelfInteractionRatios",
    "reduceHiCDOCDataSet",
    "sampleConditions",
    "sampleReplicates",
    "show"
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      "title": "Example HiCDOCDataSet.",
      "object": "exampleHiCDOCDataSet",
      "file": "exampleHiCDOCDataSet.rda",
      "class": [
        "HiCDOCDataSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "exampleHiCDOCDataSetProcessed",
      "title": "Example HiCDOCDataSet, filtered, normalized and with compartements detected.",
      "object": "exampleHiCDOCDataSetProcessed",
      "file": "exampleHiCDOCDataSetProcessed.rda",
      "class": [
        "HiCDOCDataSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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    {
      "page": "HiCDOC-package",
      "title": "A/B compartment detection and differential analysis",
      "topics": [
        "HiCDOC-package"
      ]
    },
    {
      "page": "detectCompartments",
      "title": "A and B compartments detection and differences across conditions.",
      "topics": [
        "detectCompartments"
      ]
    },
    {
      "page": "exampleHiCDOCDataSet",
      "title": "Example HiCDOCDataSet.",
      "topics": [
        "exampleHiCDOCDataSet"
      ]
    },
    {
      "page": "exampleHiCDOCDataSetProcessed",
      "title": "Example HiCDOCDataSet, filtered, normalized and with compartements detected.",
      "topics": [
        "exampleHiCDOCDataSetProcessed"
      ]
    },
    {
      "page": "filterSmallChromosomes",
      "title": "Filter small chromosomes.",
      "topics": [
        "filterSmallChromosomes"
      ]
    },
    {
      "page": "filterSparseReplicates",
      "title": "Filter sparse replicates.",
      "topics": [
        "filterSparseReplicates"
      ]
    },
    {
      "page": "filterWeakPositions",
      "title": "Filter weak positions.",
      "topics": [
        "filterWeakPositions"
      ]
    },
    {
      "page": "HiCDOC",
      "title": "Default pipeline to run on the HiCDOC analysis.",
      "topics": [
        "HiCDOC"
      ]
    },
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      "page": "HiCDOCDataSet-class",
      "title": "'HiCDOCDataSet' S4 class.",
      "topics": [
        "HiCDOCDataSet",
        "HiCDOCDataSet-class"
      ]
    },
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      "title": "Methods to access a 'HiCDOCDataSet' components.",
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        "chromosomes,HiCDOCDataSet-method",
        "compartments",
        "compartments,HiCDOCDataSet-method",
        "concordances",
        "concordances,HiCDOCDataSet-method",
        "differences",
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        "HiCDOCDataSet-methods",
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        "sampleConditions,HiCDOCDataSet-method",
        "sampleReplicates",
        "sampleReplicates,HiCDOCDataSet-method",
        "show,HiCDOCDataSet-method"
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        "HiCDOCDataSet-parameters",
        "parameters",
        "parameters,HiCDOCDataSet-method",
        "parameters<-",
        "parameters<-,HiCDOCDataSet-method"
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      "title": "'HiCDOCDataSet' constructor from Cool files.",
      "topics": [
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      "topics": [
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      "title": "Normalize biological biases.",
      "topics": [
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      "title": "Normalize distance effect.",
      "topics": [
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      "title": "Normalize technical biases.",
      "topics": [
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      "title": "Plot centroids.",
      "topics": [
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      "title": "Plot compartment changes.",
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      "title": "Plot A/B compartments.",
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      "topics": [
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        "Tabular files",
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        "HiC-Pro files",
        "Running the HiCDOC pipeline",
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