{
  "_id": "6a1bddbf1d7bb097a0a1787c",
  "Package": "breakpointR",
  "Type": "Package",
  "Title": "Find breakpoints in Strand-seq data",
  "Version": "1.30.0",
  "Date": "2021-11-20",
  "Author": "David Porubsky, Ashley Sanders, Aaron Taudt",
  "Maintainer": "David Porubsky <david.porubsky@gmail.com>",
  "Description": "This package implements functions for finding breakpoints,\nplotting and export of Strand-seq data.",
  "License": "file LICENSE",
  "LazyLoad": "yes",
  "VignetteBuilder": "knitr",
  "Packaged": {
    "Date": "2026-05-31 06:31:35 UTC",
    "User": "root"
  },
  "biocViews": "Software, Sequencing, DNASeq, SingleCell, Coverage",
  "URL": "https://github.com/daewoooo/BreakPointR",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:44 UTC",
  "RemoteUrl": "https://github.com/bioc/breakpointR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
  "NeedsCompilation": "no",
  "MD5sum": "a888cd5ab58495ab7219169072681627",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "breakpointR_1.30.0.tar.gz",
  "_fileid": "2a85adfdd4f7efe5895581d1b49a000c5135a22062bf67fa247cc1307cbde8fc",
  "_filesize": 991443,
  "_sha256": "2a85adfdd4f7efe5895581d1b49a000c5135a22062bf67fa247cc1307cbde8fc",
  "_created": "2026-05-31T06:31:35.000Z",
  "_published": "2026-05-31T07:05:35.740Z",
  "_jobs": [
    {
      "job": 78705753984,
      "time": 161,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314465338"
    },
    {
      "job": 78705753990,
      "time": 356,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314488037"
    },
    {
      "job": 78705753991,
      "time": 384,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314491180"
    },
    {
      "job": 78705753992,
      "time": 257,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314654574"
    },
    {
      "job": 78705754004,
      "time": 260,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314646928"
    },
    {
      "job": 78705459278,
      "time": 320,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314446896"
    },
    {
      "job": 78705753985,
      "time": 145,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314463391"
    },
    {
      "job": 78705754005,
      "time": 306,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314482307"
    },
    {
      "job": 78705753999,
      "time": 293,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314480869"
    },
    {
      "job": 78705754001,
      "time": 288,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314479989"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/breakpointR",
  "_commit": {
    "id": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
    "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": 1777380524
  },
  "_maintainer": {
    "name": "David Porubsky",
    "email": "david.porubsky@gmail.com",
    "login": "daewoooo",
    "description": "",
    "uuid": 7230521
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "cowplot",
      "role": "Depends"
    },
    {
      "package": "breakpointRdata",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "version": ">= 1.12.3",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "sequencing",
    "dnaseq",
    "singlecell",
    "coverage"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "daewoooo",
      "count": 47,
      "uuid": 7230521
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "drashley",
      "count": 3,
      "uuid": 14876198
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 446,
    "source": "https://www.bioconductor.org/packages/stats/bioc/breakpointR"
  },
  "_devurl": "https://github.com/daewoooo/breakpointr",
  "_searchresults": 19,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/breakpointR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/daewoooo/breakpointr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "breakpointr",
    "breakpointr2UCSC",
    "breakSeekr",
    "deltaWCalculator",
    "exportRegions",
    "genotype.binom",
    "genotype.fisher",
    "GenotypeBreaks",
    "hotspotter",
    "loadFromFiles",
    "plotBreakpoints",
    "plotBreakpointsPerChr",
    "plotHeatmap",
    "ranges2UCSC",
    "readBamFileAsGRanges",
    "removeReadPileupSpikes",
    "runBreakpointr",
    "summarizeBreaks",
    "synchronizeReadDir"
  ],
  "_help": [
    {
      "page": "breakpointR-package",
      "title": "Breakpoint detection in Strand-Seq data",
      "topics": [
        "breakpointR-package",
        "breakpointR"
      ]
    },
    {
      "page": "BreakPoint",
      "title": "BreakPoint object",
      "topics": [
        "BreakPoint"
      ]
    },
    {
      "page": "breakpointr",
      "title": "Main function for the 'breakpointR' package",
      "topics": [
        "breakpointr"
      ]
    },
    {
      "page": "breakpointr2UCSC",
      "title": "Export UCSC browser formated files",
      "topics": [
        "breakpointr2UCSC"
      ]
    },
    {
      "page": "breakSeekr",
      "title": "Find breakpoints from deltaWs",
      "topics": [
        "breakSeekr"
      ]
    },
    {
      "page": "collapseBins",
      "title": "Collapse consecutive bins with the same ID value",
      "topics": [
        "collapseBins"
      ]
    },
    {
      "page": "confidenceInterval",
      "title": "Estimate confidence intervals for breakpoints",
      "topics": [
        "confidenceInterval"
      ]
    },
    {
      "page": "confidenceInterval.binomial",
      "title": "Estimate confidence intervals for breakpoints",
      "topics": [
        "confidenceInterval.binomial"
      ]
    },
    {
      "page": "createCompositeFile",
      "title": "Create composite Strand-seq file",
      "topics": [
        "createCompositeFile"
      ]
    },
    {
      "page": "deltaWCalculator",
      "title": "Calculate deltaWs",
      "topics": [
        "deltaWCalculator"
      ]
    },
    {
      "page": "deltaWCalculatorVariousWindows",
      "title": "Calculate deltaWs using various window sizes",
      "topics": [
        "deltaWCalculatorVariousWindows"
      ]
    },
    {
      "page": "exportRegions",
      "title": "Function to print WC regions after breakpointR analysis",
      "topics": [
        "exportRegions"
      ]
    },
    {
      "page": "genotype.binom",
      "title": "Assign states to any given region using binomial test.",
      "topics": [
        "genotype.binom"
      ]
    },
    {
      "page": "genotype.fisher",
      "title": "Assign states to any given region using Fisher Exact Test.",
      "topics": [
        "genotype.fisher"
      ]
    },
    {
      "page": "genotyping",
      "title": "Set of functions to genotype regions in between localized breakpoints",
      "topics": [
        "GenotypeBreaks",
        "genotyping"
      ]
    },
    {
      "page": "hotspotter",
      "title": "Find hotspots of genomic events",
      "topics": [
        "hotspotter"
      ]
    },
    {
      "page": "insertchr",
      "title": "Insert chromosome for in case it's missing",
      "topics": [
        "insertchr"
      ]
    },
    {
      "page": "loadFromFiles",
      "title": "Load 'breakpointR' objects from file",
      "topics": [
        "loadFromFiles"
      ]
    },
    {
      "page": "plotBreakpoints",
      "title": "Plotting genome-wide ideograms 'breakpointR'",
      "topics": [
        "plotBreakpoints"
      ]
    },
    {
      "page": "plotBreakpointsPerChr",
      "title": "Plotting chromosome specific ideograms 'breakpointR'",
      "topics": [
        "plotBreakpointsPerChr"
      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Genome wide heatmap of template inheritance states",
      "topics": [
        "plotHeatmap"
      ]
    },
    {
      "page": "ranges2UCSC",
      "title": "Generates a bedfile from an input GRanges file",
      "topics": [
        "ranges2UCSC"
      ]
    },
    {
      "page": "readBamFileAsGRanges",
      "title": "Import BAM file into GRanges",
      "topics": [
        "readBamFileAsGRanges"
      ]
    },
    {
      "page": "readConfig",
      "title": "Read breakpointR configuration file",
      "topics": [
        "readConfig"
      ]
    },
    {
      "page": "removeDoubleSCEs",
      "title": "Process double SCE chromosomes: with internal WC region.",
      "topics": [
        "removeDoubleSCEs"
      ]
    },
    {
      "page": "removeReadPileupSpikes",
      "title": "Remove large spikes in short reads coverage",
      "topics": [
        "removeReadPileupSpikes"
      ]
    },
    {
      "page": "runBreakpointr",
      "title": "Find breakpoints in Strand-seq data",
      "topics": [
        "runBreakpointr"
      ]
    },
    {
      "page": "summarizeBreaks",
      "title": "Compile breakpoint summary table",
      "topics": [
        "summarizeBreaks"
      ]
    },
    {
      "page": "synchronizeReadDir",
      "title": "Synchronize Strand-seq read directionality",
      "topics": [
        "synchronizeReadDir"
      ]
    },
    {
      "page": "transCoord",
      "title": "Transform genomic coordinates",
      "topics": [
        "transCoord"
      ]
    },
    {
      "page": "writeConfig",
      "title": "Write breakpointR configuration file",
      "topics": [
        "writeConfig"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/breakpointR/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "breakpointRdata",
    "cigarillo",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "doParallel",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "httr",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RColorBrewer",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "UCSC.utils",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "breakpointR.Rnw",
      "filename": "breakpointR.pdf",
      "title": "How to use breakpointR",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2017-03-31 06:50:28",
      "modified": "2019-08-04 00:09:24",
      "commits": 6
    }
  ],
  "_score": 5.931966114728173,
  "_indexed": false,
  "_nocasepkg": "breakpointr",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/breakpointR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-05-31T06:35:22.000Z",
      "distro": "noble",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "9f41800cde9d744c2cd23f48380239ce5e4b4e76cbb43340ce67da5d146ce617",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-05-31T06:35:33.000Z",
      "distro": "noble",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "76b36ae0ac59fae0a2675cfa45e1ac0c79ae6574a21285157cbc19ff07dd7aea",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-05-31T07:02:44.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "e7e9a43b4dd790aeeb8336f842ef2aa4358e29f19d4802d085751bb049c55e76",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-05-31T07:01:14.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "c01cc70d7e95b8015cb13c494112126942f468c049661c1cfbbce590eced9665",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.30.0",
      "date": "2026-05-31T06:34:38.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "8a2264712ba52e603ca96d1f161bffa9efabfac16d0022b2e75b35a2b2192048",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-05-31T06:33:49.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "7f7714fcc3a4bc3bba69f576d844fb32a749e14974a6f56575eb66ae19936794",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-05-31T06:33:59.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "3cfee55ab924a9b9026f4502a71f59f1a9bbf209e2073db78671b9ed8d6a59ef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-05-31T06:33:44.000Z",
      "commit": "c6194609a7d18bf9f3b8a2e0038664da7430300d",
      "fileid": "bd68179ac6349795b43e794e539a48f9e8005ed07cd89d1f393775f96edaffba",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705344497"
    }
  ]
}