{
  "_id": "6a1c0a281d7bb097a0a2cc99",
  "Package": "PeakSegDP",
  "Maintainer": "Toby Dylan Hocking <toby.hocking@r-project.org>",
  "Author": "Toby Dylan Hocking, Guillem Rigaill",
  "Version": "2024.1.24",
  "License": "GPL-3",
  "URL": "https://github.com/tdhock/PeakSegDP",
  "BugReports": "https://github.com/tdhock/PeakSegDP/issues",
  "Title": "Dynamic Programming Algorithm for Peak Detection in ChIP-Seq\nData",
  "Description": "A quadratic time dynamic programming algorithm can be used\nto compute an approximate solution to the problem of finding\nthe most likely changepoints with respect to the Poisson\nlikelihood, subject to a constraint on the number of segments,\nand the changes which must alternate: up, down, up, down, etc.\nFor more info read\n<http://proceedings.mlr.press/v37/hocking15.html> \"PeakSeg:\nconstrained optimal segmentation and supervised penalty\nlearning for peak detection in count data\" by TD Hocking et al,\nproceedings of ICML2015.",
  "Repository": "https://tdhock.r-universe.dev",
  "Date/Publication": "2024-01-24 18:48:29 UTC",
  "RemoteUrl": "https://github.com/tdhock/peaksegdp",
  "RemoteRef": "HEAD",
  "RemoteSha": "618128bb8163323bfa68ad75e24f5ca790b61371",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-31 10:11:12 UTC",
    "User": "root"
  },
  "MD5sum": "618c07d20952236dc512a294bd7e02db",
  "_user": "tdhock",
  "_type": "src",
  "_file": "PeakSegDP_2024.1.24.tar.gz",
  "_fileid": "b79dcbfdee8735c27c3e07d8b2aead0a749d6c3d3667ac1e38c8694b0b2acfdf",
  "_filesize": 623005,
  "_sha256": "b79dcbfdee8735c27c3e07d8b2aead0a749d6c3d3667ac1e38c8694b0b2acfdf",
  "_created": "2026-05-31T10:11:12.000Z",
  "_published": "2026-05-31T10:15:04.530Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78717713550,
      "time": 103,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7315872787"
    },
    {
      "job": 78717713566,
      "time": 132,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7315875647"
    },
    {
      "job": 78717713579,
      "time": 108,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315873248"
    },
    {
      "job": 78717713551,
      "time": 109,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315873401"
    },
    {
      "job": 78717713568,
      "time": 96,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7315871975"
    },
    {
      "job": 78717713557,
      "time": 132,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7315875580"
    },
    {
      "job": 78717713563,
      "time": 92,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315871784"
    },
    {
      "job": 78717713555,
      "time": 196,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315881810"
    },
    {
      "job": 78717568979,
      "time": 160,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315862319"
    },
    {
      "job": 78717713581,
      "time": 92,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315871739"
    },
    {
      "job": 78717713552,
      "time": 66,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7315869298"
    },
    {
      "job": 78717713564,
      "time": 74,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7315870221"
    },
    {
      "job": 78717713570,
      "time": 74,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7315870060"
    }
  ],
  "_buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/tdhock/peaksegdp",
  "_commit": {
    "id": "618128bb8163323bfa68ad75e24f5ca790b61371",
    "author": "Toby Dylan Hocking <Toby.Hocking@nau.edu>",
    "committer": "Toby Dylan Hocking <Toby.Hocking@nau.edu>",
    "message": "fix for CRAN\n",
    "time": 1706122109
  },
  "_maintainer": {
    "name": "Toby Dylan Hocking",
    "email": "toby.hocking@r-project.org",
    "login": "tdhock",
    "orcid": "0000-0002-3146-0865",
    "description": "",
    "uuid": 932850
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.0",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "penaltyLearning",
      "role": "Suggests"
    }
  ],
  "_owner": "tdhock",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "tdhock",
      "count": 166,
      "uuid": 932850
    },
    {
      "user": "rishit-dagli",
      "count": 1,
      "uuid": 39672672
    }
  ],
  "_userbio": {
    "uuid": 932850,
    "type": "user",
    "name": "Toby Dylan Hocking"
  },
  "_downloads": {
    "count": 747,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PeakSegDP"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/tdhock/peaksegdp",
  "_searchresults": 25,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PeakSegDP.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tdhock/peaksegdp",
  "_realowner": "tdhock",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2017.06.20",
      "date": "2017-06-20"
    },
    {
      "version": "2017.08.15",
      "date": "2017-08-15"
    },
    {
      "version": "2024.1.24",
      "date": "2024-01-24"
    }
  ],
  "_exports": [
    "cDPA",
    "getPath",
    "PeakSegDP",
    "PoissonLoss"
  ],
  "_datasets": [
    {
      "name": "chr11ChIPseq",
      "title": "ChIP-seq aligned read coverage for 4 samples on a subset of chr11",
      "object": "chr11ChIPseq",
      "file": "chr11ChIPseq.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "chr11first",
      "title": "Counts of first base of aligned reads",
      "object": "chr11first",
      "file": "chr11first.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 23252,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K36me3.AM.immune.19",
      "title": "Several ChIP-seq profiles, some of which have few data points",
      "object": "H3K36me3.AM.immune.19",
      "file": "H3K36me3.AM.immune.19.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K36me3.TDH.other.chunk3.cluster4",
      "title": "8 profiles of H3K36me3 data",
      "object": "H3K36me3.TDH.other.chunk3.cluster4",
      "file": "H3K36me3.TDH.other.chunk3.cluster4.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 36914,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K4me3.TDH.immune.chunk12.cluster4",
      "title": "Histone ChIP-seq data, 26 samples, chr1 subset",
      "object": "H3K4me3.TDH.immune.chunk12.cluster4",
      "file": "H3K4me3.TDH.immune.chunk12.cluster4.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 20199,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calc.grad.list",
      "title": "calc grad list",
      "topics": [
        "calc.grad.list"
      ]
    },
    {
      "page": "calc.loss.from.lp.list",
      "title": "calc loss from lp list",
      "topics": [
        "calc.loss.from.lp.list"
      ]
    },
    {
      "page": "calc.loss.list",
      "title": "calc loss list",
      "topics": [
        "calc.loss.list"
      ]
    },
    {
      "page": "cDPA",
      "title": "cDPA",
      "topics": [
        "cDPA"
      ]
    },
    {
      "page": "chr11ChIPseq",
      "title": "ChIP-seq aligned read coverage for 4 samples on a subset of chr11",
      "topics": [
        "chr11ChIPseq"
      ]
    },
    {
      "page": "chr11first",
      "title": "Counts of first base of aligned reads",
      "topics": [
        "chr11first"
      ]
    },
    {
      "page": "derivs",
      "title": "derivs",
      "topics": [
        "derivs"
      ]
    },
    {
      "page": "GeomTallRect",
      "title": "GeomTallRect",
      "topics": [
        "GeomTallRect"
      ]
    },
    {
      "page": "getPath",
      "title": "getPath",
      "topics": [
        "getPath"
      ]
    },
    {
      "page": "H3K36me3.AM.immune.19",
      "title": "Several ChIP-seq profiles, some of which have few data points",
      "topics": [
        "H3K36me3.AM.immune.19"
      ]
    },
    {
      "page": "H3K36me3.TDH.other.chunk3.cluster4",
      "title": "8 profiles of H3K36me3 data",
      "topics": [
        "H3K36me3.TDH.other.chunk3.cluster4"
      ]
    },
    {
      "page": "H3K4me3.TDH.immune.chunk12.cluster4",
      "title": "Histone ChIP-seq data, 26 samples, chr1 subset",
      "topics": [
        "H3K4me3.TDH.immune.chunk12.cluster4"
      ]
    },
    {
      "page": "PeakSegDP",
      "title": "PeakSegDP",
      "topics": [
        "PeakSegDP"
      ]
    },
    {
      "page": "phi.list",
      "title": "phi list",
      "topics": [
        "phi.list"
      ]
    },
    {
      "page": "PoissonLoss",
      "title": "PoissonLoss",
      "topics": [
        "PoissonLoss"
      ]
    },
    {
      "page": "regression.funs",
      "title": "regression funs",
      "topics": [
        "regression.funs"
      ]
    }
  ],
  "_rundeps": [],
  "_score": 2.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "peaksegdp",
  "_universes": [
    "tdhock"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:02.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "0e529e1180967b794ee88fff765c1d9dbc76a5e01c5902fc2fc3665a04a35702",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:26.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "bf7cca0b2cf080022ef6c6e1607dd358dce7bc4e41555fdeb5a0fb3daf572dcc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:09.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "e1c8a4f5a11f4bdf238ef4f615929929b8e5622230cdfcf2f3983d1881ba1900",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:07.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "5da77fedf1eac84e90a66e22a7857ea2b77da114ce9114f467b567c9c7838480",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.1.24",
      "date": "2026-05-31T10:12:52.000Z",
      "arch": "aarch64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "321ca61e3dabf7677c39b638a2394b1aa596ce81cabf6147b9cba271cf81c3ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:24.000Z",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "1af5347c8079f827114923a37565ec1e5c9fa612786a774d0e5ab7c15736379d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2024.1.24",
      "date": "2026-05-31T10:12:50.000Z",
      "arch": "aarch64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "1f453043151b4fb03e67a11f4d6471b8789f1459a1297e6c61322afccb946281",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2024.1.24",
      "date": "2026-05-31T10:14:26.000Z",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "1f1dcbb8c149d6ff54adcc8a8c4d1cccb4d91d8157ed33c4629775694516ef7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2024.1.24",
      "date": "2026-05-31T10:13:01.000Z",
      "arch": "emscripten",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "13d8e787588793aff4c5aa6f54e5fa0d19090fb8d9bb90ac4a4f0c4d4a9a9df8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2024.1.24",
      "date": "2026-05-31T10:12:15.000Z",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "260653a3d8bbab707a009cd6c223087d7bf1c60122473d5c3fe91f010de22d12",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2024.1.24",
      "date": "2026-05-31T10:12:23.000Z",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "8df35b5e750192b51397c1f35543eafdb111607e99d9b0c95cca4f4062686a1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2024.1.24",
      "date": "2026-05-31T10:12:24.000Z",
      "arch": "x86_64",
      "commit": "618128bb8163323bfa68ad75e24f5ca790b61371",
      "fileid": "c1cd1734309662e2d4c660179179ca55b0f774eb919c46f24fc32c6fce630080",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/26709721527"
    }
  ]
}