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  "Title": "HiCaptuRe: Manipulating and integrating Capture Hi-C data",
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  "Description": "Capture Hi-C is a set of techniques that enable the\ndetection of genomic interactions involving regions of\ninterest, known as baits. By focusing on selected loci, these\napproaches reduce sequencing costs while maintaining high\nresolution at the level of restriction fragments. HiCaptuRe\nprovides tools to import, annotate, manipulate, and export\nCapture Hi-C data. The package accounts for the specific\nstructure of bait–otherEnd interactions, facilitates\nintegration with other omics datasets, and enables comparison\nacross samples and conditions.",
  "BugReports": "https://github.com/LaureTomas/HiCaptuRe/issues",
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  "Date/Publication": "2026-04-28 13:05:20 UTC",
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      "title": "Annotates HiCaptuRe object from load_interactions",
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      "topics": [
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      "page": "getters",
      "title": "Internal functions to access data held in a HiCaptuRe object.",
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        "getByBaits,HiCaptuRe-method",
        "getByRegions",
        "getByRegions,HiCaptuRe-method",
        "getParameters",
        "getParameters,HiCaptuRe-method",
        "getters"
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      "title": "HiCaptuRe Class",
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      ]
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      "page": "interactionsByBaits",
      "title": "Filters HiCaptuRe object by baits",
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        "interactionsByBaits"
      ]
    },
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      "page": "interactionsByRegions",
      "title": "Filters HiCaptuRe object by overlaping regions",
      "topics": [
        "interactionsByRegions"
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      "title": "Creates a list of HiCaptuRe objects based on a peakmatrix",
      "topics": [
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    },
    {
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      "title": "Generate the plot based on distance output",
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      "headings": [
        "Overview",
        "Importing Interaction Data: load_interactions()",
        "What is a HiCaptuRe object?",
        "Inspecting the HiCaptuRe Object",
        "Tracking Parameters Used in Each Step",
        "Digesting the Genome: digest_genome()",
        "Enzyme Parameters",
        "Controlling Genome Digestion",
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        "Annotating Interactions: annotate_interactions()",
        "Filtering Interactions",
        "Filtering interactions by Baits of interest: interactionsByBaits()",
        "Bait Summary: getByBaits()",
        "Filtering by Genomic Regions: interactionsByRegions()",
        "Regions Summary: getByRegions()",
        "Intersecting Interaction Sets: intersect_interactions()",
        "Summarizing Interaction Distances: distance_summary",
        "Visualizing Distance Distributions: plot_distance_summary()",
        "Extracting Interactions from a peakmatrix: peakmatrix2list()",
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      "filename": "vignetteIntroduction.html",
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        "Overview",
        "Motivation for Bioconductor",
        "Basic Vocabulary",
        "Data Origin and Experimental Workflow",
        "Capture Hi-C Data Formats (some CHiCAGO outputs)",
        "interBed - ibed — Recommended Format",
        "peakmatrix — Multi-sample Interaction Matrix",
        "seqMonk — Two-row Interaction Format",
        "**bedpe ** — Generic Paired-End Interaction Format",
        "**washU ** — Minimal Format for Browser Upload",
        "**washUold ** — (Legacy)",
        "Summary",
        "The HiCaptuRe Object",
        "Typical Workflow",
        "Example Data",
        "📚  References",
        "SessionInfo"
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      "modified": "2025-08-11 10:21:32",
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