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  "Package": "HiCBricks",
  "Title": "Framework for Storing and Accessing Hi-C Data Through HDF Files",
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  "Description": "HiCBricks is a library designed for handling large\nhigh-resolution Hi-C datasets. Over the years, the Hi-C field\nhas experienced a rapid increase in the size and complexity of\ndatasets. HiCBricks is meant to overcome the challenges related\nto the analysis of such large datasets within the R\nenvironment. HiCBricks offers user-friendly and efficient\nsolutions for handling large high-resolution Hi-C datasets. The\npackage provides an R/Bioconductor framework with the bricks to\nbuild more complex data analysis pipelines and algorithms.\nHiCBricks already incorporates example algorithms for calling\ndomain boundaries and functions for high quality data\nvisualization.",
  "Date": "2025-07-22",
  "Type": "Package",
  "Author": "Koustav Pal [aut, cre], Carmen Livi [ctb], Ilario Tagliaferri\n[ctb]",
  "Maintainer": "Koustav Pal <koustav.pal@ifom.eu>",
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    "Brick_call_compartments",
    "Brick_export_to_sparse",
    "Brick_fetch_range_index",
    "Brick_fetch_row_vector",
    "Brick_get_bintable",
    "Brick_get_chrominfo",
    "Brick_get_entire_matrix",
    "Brick_get_matrix",
    "Brick_get_matrix_mcols",
    "Brick_get_matrix_within_coords",
    "Brick_get_ranges",
    "Brick_get_values_by_distance",
    "Brick_get_vector_values",
    "Brick_list_matrices",
    "Brick_list_matrix_mcols",
    "Brick_list_mcool_normalisations",
    "Brick_list_mcool_resolutions",
    "Brick_list_rangekeys",
    "Brick_list_ranges_mcols",
    "Brick_load_cis_matrix_till_distance",
    "Brick_load_data_from_mcool",
    "Brick_load_data_from_sparse",
    "Brick_load_matrix",
    "Brick_local_score_differentiator",
    "Brick_make_ranges",
    "Brick_matrix_dimensions",
    "Brick_matrix_exists",
    "Brick_matrix_filename",
    "Brick_matrix_isdone",
    "Brick_matrix_issparse",
    "Brick_matrix_maxdist",
    "Brick_matrix_minmax",
    "Brick_mcool_normalisation_exists",
    "Brick_rangekey_exists",
    "Brick_return_region_position",
    "Brick_vizart_plot_heatmap",
    "BrickContainer_change_experiment_name",
    "BrickContainer_change_output_directory",
    "BrickContainer_get_path_to_file",
    "BrickContainer_list_chromosomes",
    "BrickContainer_list_experiment_name",
    "BrickContainer_list_files",
    "BrickContainer_list_output_directory",
    "BrickContainer_list_resolutions",
    "BrickContainer_unlink_resolution",
    "Create_many_Bricks",
    "Create_many_Bricks_from_mcool",
    "load_BrickContainer"
  ],
  "_help": [
    {
      "page": "Brick_add_ranges",
      "title": "Store a ranges object in the Brick store.",
      "topics": [
        "Brick_add_ranges"
      ]
    },
    {
      "page": "Brick_call_compartments",
      "title": "Identify compartments in the Hi-C data",
      "topics": [
        "Brick_call_compartments"
      ]
    },
    {
      "page": "Brick_export_to_sparse",
      "title": "Export an entire resolution from a given BrickContainer as a upper triangle sparse matrix",
      "topics": [
        "Brick_export_to_sparse"
      ]
    },
    {
      "page": "Brick_fetch_range_index",
      "title": "Returns the position of the supplied ranges in the binning table associated to the Hi-C experiment.",
      "topics": [
        "Brick_fetch_range_index"
      ]
    },
    {
      "page": "Brick_fetch_row_vector",
      "title": "Return row or col vectors.",
      "topics": [
        "Brick_fetch_row_vector"
      ]
    },
    {
      "page": "Brick_get_bintable",
      "title": "Returns the binning table associated to the Hi-C experiment.",
      "topics": [
        "Brick_get_bintable"
      ]
    },
    {
      "page": "Brick_get_chrominfo",
      "title": "Get the chrominfo for the Hi-C experiment.",
      "topics": [
        "Brick_get_chrominfo"
      ]
    },
    {
      "page": "Brick_get_entire_matrix",
      "title": "Return an entire matrix for provided chromosome pair for a resolution.",
      "topics": [
        "Brick_get_entire_matrix"
      ]
    },
    {
      "page": "Brick_get_matrix",
      "title": "Return a matrix subset.",
      "topics": [
        "Brick_get_matrix"
      ]
    },
    {
      "page": "Brick_get_matrix_mcols",
      "title": "Get the matrix metadata columns in the Brick store.",
      "topics": [
        "Brick_get_matrix_mcols"
      ]
    },
    {
      "page": "Brick_get_matrix_within_coords",
      "title": "Return a matrix subset between two regions.",
      "topics": [
        "Brick_get_matrix_within_coords"
      ]
    },
    {
      "page": "Brick_get_ranges",
      "title": "Fetch the ranges associated to a rangekey or chromosome.",
      "topics": [
        "Brick_get_ranges"
      ]
    },
    {
      "page": "Brick_get_values_by_distance",
      "title": "Return values separated by a certain distance.",
      "topics": [
        "Brick_get_values_by_distance"
      ]
    },
    {
      "page": "Brick_get_vector_values",
      "title": "Return a N dimensional vector selection.",
      "topics": [
        "Brick_get_vector_values"
      ]
    },
    {
      "page": "Brick_list_matrices",
      "title": "List the matrix pairs present in the Brick store.",
      "topics": [
        "Brick_list_matrices"
      ]
    },
    {
      "page": "Brick_list_matrix_mcols",
      "title": "List the matrix metadata columns in the Brick store.",
      "topics": [
        "Brick_list_matrix_mcols"
      ]
    },
    {
      "page": "Brick_list_mcool_normalisations",
      "title": "Get all available normalisations in an mcool file.",
      "topics": [
        "Brick_list_mcool_normalisations"
      ]
    },
    {
      "page": "Brick_list_mcool_resolutions",
      "title": "Get all available normalisations in an mcool file.",
      "topics": [
        "Brick_list_mcool_resolutions"
      ]
    },
    {
      "page": "Brick_list_rangekeys",
      "title": "List the ranges tables stored within the Brick.",
      "topics": [
        "Brick_list_rangekeys"
      ]
    },
    {
      "page": "Brick_list_ranges_mcols",
      "title": "Find out what metadata columns are associated to a ranges with a certain name",
      "topics": [
        "Brick_list_ranges_mcols"
      ]
    },
    {
      "page": "Brick_load_cis_matrix_till_distance",
      "title": "Load a NxN dimensional sub-distance _cis_ matrix into the Brick store.",
      "topics": [
        "Brick_load_cis_matrix_till_distance"
      ]
    },
    {
      "page": "Brick_load_data_from_mcool",
      "title": "Load a NxN dimensional matrix into the Brick store from an mcool file.",
      "topics": [
        "Brick_load_data_from_mcool"
      ]
    },
    {
      "page": "Brick_load_data_from_sparse",
      "title": "Identify compartments in the Hi-C data",
      "topics": [
        "Brick_load_data_from_sparse"
      ]
    },
    {
      "page": "Brick_load_matrix",
      "title": "Load a NxM dimensional matrix into the Brick store.",
      "topics": [
        "Brick_load_matrix"
      ]
    },
    {
      "page": "Brick_local_score_differentiator",
      "title": "Do TAD Calls with Local Score Differentiator on a Hi-C matrix",
      "topics": [
        "Brick_local_score_differentiator"
      ]
    },
    {
      "page": "Brick_make_ranges",
      "title": "Creates a ranges object from provided vectors.",
      "topics": [
        "Brick_make_ranges"
      ]
    },
    {
      "page": "Brick_matrix_dimensions",
      "title": "Return the dimensions of a matrix",
      "topics": [
        "Brick_matrix_dimensions"
      ]
    },
    {
      "page": "Brick_matrix_exists",
      "title": "Check if a chromosome pair exists.",
      "topics": [
        "Brick_matrix_exists"
      ]
    },
    {
      "page": "Brick_matrix_filename",
      "title": "Return the filename of the loaded matrix",
      "topics": [
        "Brick_matrix_filename"
      ]
    },
    {
      "page": "Brick_matrix_isdone",
      "title": "Check if a matrix has been loaded for a chromosome pair.",
      "topics": [
        "Brick_matrix_isdone"
      ]
    },
    {
      "page": "Brick_matrix_issparse",
      "title": "Check if a matrix for a chromosome pair is sparse.",
      "topics": [
        "Brick_matrix_issparse"
      ]
    },
    {
      "page": "Brick_matrix_maxdist",
      "title": "Get the maximum loaded distance from the diagonal of any matrix.",
      "topics": [
        "Brick_matrix_maxdist"
      ]
    },
    {
      "page": "Brick_matrix_minmax",
      "title": "Return the value range of the matrix",
      "topics": [
        "Brick_matrix_minmax"
      ]
    },
    {
      "page": "Brick_mcool_normalisation_exists",
      "title": "Check if a normalisation exists in an mcool file.",
      "topics": [
        "Brick_mcool_normalisation_exists"
      ]
    },
    {
      "page": "Brick_rangekey_exists",
      "title": "Check to see if the Brick contains a ranges with a certain name.",
      "topics": [
        "Brick_rangekey_exists"
      ]
    },
    {
      "page": "Brick_return_region_position",
      "title": "Provides the overlapping position (within) from the bintable.",
      "topics": [
        "Brick_return_region_position"
      ]
    },
    {
      "page": "Brick_vizart_plot_heatmap",
      "title": "Create the entire HDF5 structure and load the bintable",
      "topics": [
        "Brick_vizart_plot_heatmap"
      ]
    },
    {
      "page": "BrickContainer_change_experiment_name",
      "title": "Change the location of HDF files in the BrickContainer object",
      "topics": [
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      ]
    },
    {
      "page": "BrickContainer_change_output_directory",
      "title": "Change the location of HDF files in the BrickContainer object",
      "topics": [
        "BrickContainer_change_output_directory"
      ]
    },
    {
      "page": "BrickContainer_get_path_to_file",
      "title": "Get the path to HDF files present in the Brick container.",
      "topics": [
        "BrickContainer_get_path_to_file"
      ]
    },
    {
      "page": "BrickContainer_list_chromosomes",
      "title": "Return the descriptive name of the BrickContainer",
      "topics": [
        "BrickContainer_list_chromosomes"
      ]
    },
    {
      "page": "BrickContainer_list_experiment_name",
      "title": "Return the descriptive name of the BrickContainer",
      "topics": [
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      ]
    },
    {
      "page": "BrickContainer_list_files",
      "title": "Get the list of HDF files present in the Brick container.",
      "topics": [
        "BrickContainer_list_files"
      ]
    },
    {
      "page": "BrickContainer_list_output_directory",
      "title": "Return the output directory of the BrickContainer",
      "topics": [
        "BrickContainer_list_output_directory"
      ]
    },
    {
      "page": "BrickContainer_list_resolutions",
      "title": "Return the descriptive name of the BrickContainer",
      "topics": [
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    },
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      "page": "BrickContainer_unlink_resolution",
      "title": "Remove links to all Hi-C matrices for a given resolution.",
      "topics": [
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    },
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      "topics": [
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      "title": "Create the entire HDF5 structure and load the bintable from a mcool file",
      "topics": [
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      ]
    },
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      "page": "HiCBricks",
      "title": "A package for storing, accessing and plotting Hi-C data",
      "topics": [
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    },
    {
      "page": "load_BrickContainer",
      "title": "Create a BrickContainer object from a JSON file",
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        "Introduction",
        "Create Brick objects to store Hi-C data",
        "Creating a Brick object from a text file 2D contact matrix",
        "Creating Brick objects from sparse matrices",
        "Creating Brick objects from .mcool binary files",
        "Creating Brick objects from .hic binary files",
        "Exporting data from Brick objects",
        "Converting sparse matrix to mcool",
        "Accessing data in Brick objects",
        "Accessing genomic coordinates in a Brick object",
        "Identifying matrix row/col using ranges operations",
        "Accessing contact matrices in a Brick object",
        "Retrieving points separated by a certain distance",
        "Retrieving subsets of a matrix",
        "Accessing matrix metadata columns",
        "Matrix utility functions",
        "Example analyses implemented in HiCBricks",
        "Call Topologically Associated Domains with Local score differentiator (LSD)",
        "Fetching the TAD calls from the Brick object",
        "Creating sophisticated data visualization plots using HiCBricks",
        "Plotting one sample heatmaps",
        "Plotting bipartite (two-sample) heatmaps",
        "Plotting TADs on Bipartite heatmaps",
        "Making edits to additional plot elements",
        "Modifying text elements in plots"
      ],
      "created": "2019-02-03 09:55:50",
      "modified": "2026-07-06 05:43:31",
      "commits": 25
    }
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