{
  "_id": "6a168e55acfb0bcc41d77b2a",
  "Package": "GOTHiC",
  "Title": "Binomial test for Hi-C data analysis",
  "Description": "This is a Hi-C analysis package using a cumulative\nbinomial test to detect interactions between distal genomic\nloci that have significantly more reads than expected by chance\nin Hi-C experiments. It takes mapped paired NGS reads as input\nand gives back the list of significant interactions for a given\nbin size in the genome.",
  "Version": "1.48.0",
  "Date": "2025-07-22",
  "Author": "Borbala Mifsud and Robert Sugar",
  "Maintainer": "Borbala Mifsud <b.mifsud@qmul.ac.uk>",
  "License": "GPL-3",
  "biocViews": "ImmunoOncology, Sequencing, Preprocessing, Epigenetics, HiC",
  "Config/pak/sysreqs": "make libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:28 UTC",
  "RemoteUrl": "https://github.com/bioc/GOTHiC",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "d9e409fed3a2442507c1fd7e4455accde96c063b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 06:15:53 UTC",
    "User": "root"
  },
  "MD5sum": "61e64c60a84c1a508dc4a4b2302f0eaa",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "GOTHiC_1.48.0.tar.gz",
  "_fileid": "16eaab7e22d2f29de8a67513191f4d6cad6bdaed9bdde96c0c4bc737ae6cd685",
  "_filesize": 1751414,
  "_sha256": "16eaab7e22d2f29de8a67513191f4d6cad6bdaed9bdde96c0c4bc737ae6cd685",
  "_created": "2026-05-27T06:15:53.000Z",
  "_published": "2026-05-27T06:25:24.996Z",
  "_jobs": [
    {
      "job": 78018883132,
      "time": 198,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7233278468"
    },
    {
      "job": 78018883144,
      "time": 506,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233351708"
    },
    {
      "job": 78018883138,
      "time": 475,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233343460"
    },
    {
      "job": 78018883157,
      "time": 403,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233326871"
    },
    {
      "job": 78018883147,
      "time": 311,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233303883"
    },
    {
      "job": 78018334899,
      "time": 275,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233231440"
    },
    {
      "job": 78018883146,
      "time": 145,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233266568"
    },
    {
      "job": 78018883149,
      "time": 422,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233331096"
    },
    {
      "job": 78018883150,
      "time": 355,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233314939"
    },
    {
      "job": 78018883154,
      "time": 428,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233332474"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 2,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GOTHiC",
  "_commit": {
    "id": "d9e409fed3a2442507c1fd7e4455accde96c063b",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380628
  },
  "_maintainer": {
    "name": "Borbala Mifsud",
    "email": "b.mifsud@qmul.ac.uk",
    "login": "borimifsud",
    "description": "",
    "uuid": 22659646
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.9.38",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "ShortRead",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "HiCDataLymphoblast",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Enhances"
    }
  ],
  "_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": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "sequencing",
    "preprocessing",
    "epigenetics",
    "hic"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 534,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GOTHiC"
  },
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GOTHiC.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "GOTHiC",
    "GOTHiChicup",
    "mapReadsToRestrictionSites",
    "pairReads"
  ],
  "_datasets": [
    {
      "name": "filtered",
      "title": "A GenomicRangesList object used as an example in the GOTHiC package",
      "object": "lymphoid_chr20_paired_filtered",
      "file": "lymphoid_chr20_paired_filtered.rdata",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "filtered",
      "title": "A GenomicRangesList object used as an example in the GOTHiC package",
      "topics": [
        "filtered",
        "lymphoid_chr20_paired_filtered"
      ]
    },
    {
      "page": "GOTHiC",
      "title": "Genome Organisation Through HiC",
      "topics": [
        "GOTHiC"
      ]
    },
    {
      "page": "GOTHiChicup",
      "title": "Genome Organisation Through HiC from HiCUP output",
      "topics": [
        "GOTHiChicup"
      ]
    },
    {
      "page": "mapReadsToRestrictionSites",
      "title": "Function to map aligned and paired reads to the restriction fragments",
      "topics": [
        "mapReadsToRestrictionSites"
      ]
    },
    {
      "page": "pairReads",
      "title": "Function pairs aligned paired NGS reads",
      "topics": [
        "pairReads"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DelayedArray",
    "deldir",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "httr",
    "hwriter",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lifecycle",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "png",
    "pwalign",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "ShortRead",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "package_vignettes.Snw",
      "filename": "package_vignettes.pdf",
      "title": "GOTHiC",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-19 01:22:24",
      "modified": "2015-05-07 14:20:55",
      "commits": 4
    }
  ],
  "_score": 3.4771212547196626,
  "_indexed": false,
  "_nocasepkg": "gothic",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/GOTHiC",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-05-27T06:20:15.000Z",
      "distro": "noble",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "451f2029c0b5284aead149cd580e0fe088a24f3e267f528b690adb2241dd7212",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-05-27T06:19:54.000Z",
      "distro": "noble",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "1f523c191edc3f32d2c6f9a44cbbaef3138ac60eac6043122065f975fa069b1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-05-27T06:18:11.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "16afa3bac544f75b96ffa111910ca901c9fa62f515bb0662c9a8180bbe0dd4a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-05-27T06:17:56.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "ce88c9b028a6a7c6d692aa830368dbad3c9ae00c894118d6886c54f42dac9f65",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.48.0",
      "date": "2026-05-27T06:19:00.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "33e1550d2ca0799518784bcf3dda4034a027475977a1edf318a701846235334f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-05-27T06:18:02.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "4165369932228df74af3837bd59889d2c13f518a0852889fb69604c261a627a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-05-27T06:17:53.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "8746aa20b1f580608dff5b1b543785e6484aba8d6108cb76cbea0168889343f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-05-27T06:18:26.000Z",
      "commit": "d9e409fed3a2442507c1fd7e4455accde96c063b",
      "fileid": "3fa22617fab19ee9feca1746dd5b88f3d38400ac2e93c31b7ecea5f7a2651aad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26494141744"
    }
  ]
}