{ "_id": "6a1ad73c1d7bb097a09e6218", "Package": "HiCBricks", "Title": "Framework for Storing and Accessing Hi-C Data Through HDF Files", "Version": "1.30.0", "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 ", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.0.1", "biocViews": "DataImport, Infrastructure, Software, Technology,\nSequencing, HiC", "Config/pak/sysreqs": "libicu-dev libssl-dev libx11-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:48:57 UTC", "RemoteUrl": "https://github.com/bioc/HiCBricks", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:04:20 UTC", "User": "root" }, "MD5sum": "1088ec9a4da093dea705fd3a9e23ef96", "_user": "bioc-release", "_type": "src", "_file": "HiCBricks_1.30.0.tar.gz", "_fileid": "4569db664e746c62fbb62a76de107bd47d3b0312e0ba2392107b47d1c46c9841", "_filesize": 2605115, "_sha256": "4569db664e746c62fbb62a76de107bd47d3b0312e0ba2392107b47d1c46c9841", "_created": "2026-05-30T09:04:20.000Z", "_published": "2026-05-30T12:25:32.638Z", "_jobs": [ { "job": 78638477893, "time": 195, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307062946" }, { "job": 78638477880, "time": 257, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307068682" }, { "job": 78638477878, "time": 276, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7307070371" }, { "job": 78638477887, "time": 130, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7308147607" }, { "job": 78638477886, "time": 110, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7308143345" }, { "job": 78638281607, "time": 225, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7307043269" }, { "job": 78638477881, "time": 149, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307058315" }, { "job": 78638477889, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7307060521" }, { "job": 78638477888, "time": 164, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7307059853" }, { "job": 78638477900, "time": 161, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7307059950" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/HiCBricks", "_commit": { "id": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380537 }, "_maintainer": { "name": "Koustav Pal", "email": "koustav.pal@ifom.eu", "login": "koustav-pal", "orcid": "0000-0002-6891-1148", "description": "I am a computational biologist exploring the relationships between genome architecture and functionality (transcription, translation) ", "uuid": 20904402 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "curl", "role": "Depends" }, { "package": "rhdf5", "role": "Depends" }, { "package": "R6", "role": "Depends" }, { "package": "grid", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.29.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "infrastructure", "software", "technology", "sequencing", "hic" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 516, "source": "https://www.bioconductor.org/packages/stats/bioc/HiCBricks" }, "_mentions": 1, "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HiCBricks.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "Brick_add_ranges", "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": [ "BrickContainer_change_experiment_name" ] }, { "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": [ "BrickContainer_list_experiment_name" ] }, { "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": [ "BrickContainer_list_resolutions" ] }, { "page": "BrickContainer_unlink_resolution", "title": "Remove links to all Hi-C matrices for a given resolution.", "topics": [ "BrickContainer_unlink_resolution" ] }, { "page": "Create_many_Bricks", "title": "Create the entire HDF5 structure and load the bintable", "topics": [ "Create_many_Bricks" ] }, { "page": "Create_many_Bricks_from_mcool", "title": "Create the entire HDF5 structure and load the bintable from a mcool file", "topics": [ "Create_many_Bricks_from_mcool" ] }, { "page": "HiCBricks", "title": "A package for storing, accessing and plotting Hi-C data", "topics": [ "HiCBricks" ] }, { "page": "load_BrickContainer", "title": "Create a BrickContainer object from a JSON file", "topics": [ "load_BrickContainer" ] } ], "_readme": "https://github.com/bioc/HiCBricks/raw/RELEASE_3_23/README.md", "_rundeps": [ "BH", "BiocGenerics", "biocmake", "BiocParallel", "bit", "bit64", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "digest", "dir.expiry", "farver", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "hms", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lifecycle", "magrittr", "pillar", "pkgconfig", "plyr", "prettyunits", "progress", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "readr", "reshape2", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "stringi", "stringr", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "viridis", "viridisLite", "vroom", "withr" ], "_score": 3.322219294733919, "_indexed": false, "_nocasepkg": "hicbricks", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/HiCBricks", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.30.0", "date": "2026-05-30T09:07:54.000Z", "distro": "noble", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "a8791ef1b5d85cb34cbcc744ec78f4a2dbcd41d5fa1d96396d47027d94f3ffbe", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.6.0", "os": "linux", "version": "1.30.0", "date": "2026-05-30T09:08:11.000Z", "distro": "noble", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "649d8e84225326fbdf9ea8a4a33892a2fa59c72eb096fc8969e163d10ccc12f5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.5.3", "os": "mac", "version": "1.30.0", "date": "2026-05-30T12:24:25.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "ae7c97135886f1fe87b2cb99c42412c1dae416f8ee182eac1fc7396ef9fcebca", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.6.0", "os": "mac", "version": "1.30.0", "date": "2026-05-30T12:23:43.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "4fb9d350b2ee0445638bb529511c8dfaefd393bd2a2dc5f232f0d16758efe441", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.6.0", "os": "wasm", "version": "1.30.0", "date": "2026-05-30T09:07:19.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "650d6ec41424e62e6224e37c0db88301eebacc74a47b4b45da458930c2fbbede", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.7.0", "os": "win", "version": "1.30.0", "date": "2026-05-30T09:06:24.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "856e99403751989a44d9c937fef2c8277c24d62f75d508547d999a56aba86dbd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.5.3", "os": "win", "version": "1.30.0", "date": "2026-05-30T09:06:08.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "97d58af04cec80f2d17d122414576b0b306f2297bc9d9e7ca740ebee5a3fe147", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" }, { "r": "4.6.0", "os": "win", "version": "1.30.0", "date": "2026-05-30T09:06:17.000Z", "commit": "1b10b572b099f359f4a2f445ab5d2e7285ce7f20", "fileid": "09091556970fb25dd1707e31a74935a855d15d3140c7b1784a5c6c5cf529748e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679864380" } ] }