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  "Title": "A/B compartment detection and differential analysis",
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  "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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  "Author": "Kurylo Cyril [aut],\nZytnicki Matthias [aut],\nFoissac Sylvain [aut],\nMaigné Élise [aut, cre]",
  "Maintainer": "Maigné Élise <elise.maigne@inrae.fr>",
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  "_created": "2026-09-18T19:56:58.000Z",
  "_published": "2026-09-18T20:13:49.075Z",
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      "title": "A/B compartment detection and differential analysis",
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      ]
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      "title": "A and B compartments detection and differences across conditions.",
      "topics": [
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      "title": "Example HiCDOCDataSet.",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Filter sparse replicates.",
      "topics": [
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      "title": "Filter weak positions.",
      "topics": [
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      "page": "HiCDOC",
      "title": "Default pipeline to run on the HiCDOC analysis.",
      "topics": [
        "HiCDOC"
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      "title": "'HiCDOCDataSet' S4 class.",
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        "HiCDOCDataSet-class"
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        "chromosomes,HiCDOCDataSet-method",
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        "compartments,HiCDOCDataSet-method",
        "concordances",
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      "title": "Normalize biological biases.",
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      "title": "Normalize distance effect.",
      "topics": [
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      "title": "Plot A/B compartments.",
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        "Tabular files",
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        "HiC-Pro files",
        "Running the HiCDOC pipeline",
        "Filtering data",
        "Normalizing biases",
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        "Distance effect",
        "Predicting compartments and differences",
        "Visualizing data and results",
        "Sanity checks",
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        "Compartment assignemnt",
        "Warnings",
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        "References"
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      "created": "2020-10-08 09:52:54",
      "modified": "2026-05-26 13:38:54",
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