{
  "_id": "6a5b2f7b9baadeef8ab4c558",
  "Package": "PeakSegJoint",
  "Authors@R": "person(\ngiven = c(\"Toby\", \"Dylan\"),\nfamily = \"Hocking\",\nrole = c(\"aut\", \"cre\"),\nemail = \"toby.hocking@r-project.org\")",
  "Version": "2024.12.4",
  "License": "GPL-3",
  "URL": "https://github.com/tdhock/PeakSegJoint",
  "BugReports": "https://github.com/tdhock/PeakSegJoint/issues",
  "Title": "Joint Peak Detection in Several ChIP-Seq Samples",
  "Description": "Jointly segment several ChIP-seq samples to find the peaks\nwhich are the same and different across samples. The fast\napproximate maximum Poisson likelihood algorithm is described\nin \"PeakSegJoint: fast supervised peak detection via joint\nsegmentation of multiple count data samples\"\n<doi:10.48550/arXiv.1506.01286> by TD Hocking and G Bourque.",
  "Repository": "https://tdhock.r-universe.dev",
  "Date/Publication": "2024-12-04 20:08:55 UTC",
  "RemoteUrl": "https://github.com/tdhock/peaksegjoint",
  "RemoteRef": "HEAD",
  "RemoteSha": "4d094840d3c8172409bb3af440e33d72ebbeac57",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-18 07:38:51 UTC",
    "User": "root"
  },
  "Author": "Toby Dylan Hocking [aut, cre]",
  "Maintainer": "Toby Dylan Hocking <toby.hocking@r-project.org>",
  "_user": "tdhock",
  "_type": "src",
  "_file": "PeakSegJoint_2024.12.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/89f1e7bbad786d988b9febaa0f52694f7d5634150c2a6ba57c73775c5e19a7ac",
  "_filesize": 961406,
  "_sha256": "89f1e7bbad786d988b9febaa0f52694f7d5634150c2a6ba57c73775c5e19a7ac",
  "_expires": "2026-10-26T07:47:05.000Z",
  "_created": "2026-07-18T07:38:51.000Z",
  "_published": "2026-07-18T07:47:07.503Z",
  "_jobs": [
    {
      "job": 88058620759,
      "time": 260,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8427185315"
    },
    {
      "job": 88058620776,
      "time": 273,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8427187107"
    },
    {
      "job": 88058620765,
      "time": 274,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427187425"
    },
    {
      "job": 88058620745,
      "time": 259,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427184821"
    },
    {
      "job": 88058620760,
      "time": 213,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8427178155"
    },
    {
      "job": 88058620807,
      "time": 453,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8427214539"
    },
    {
      "job": 88058620739,
      "time": 198,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427175353"
    },
    {
      "job": 88058620738,
      "time": 331,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427195921"
    },
    {
      "job": 88058388153,
      "time": 182,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427144699"
    },
    {
      "job": 88058620744,
      "time": 97,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8427160349"
    },
    {
      "job": 88058620755,
      "time": 230,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8427180165"
    },
    {
      "job": 88058620797,
      "time": 260,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8427185109"
    },
    {
      "job": 88058620783,
      "time": 247,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8427182963"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228",
  "_status": "success",
  "_upstream": "https://github.com/tdhock/peaksegjoint",
  "_commit": {
    "id": "4d094840d3c8172409bb3af440e33d72ebbeac57",
    "author": "Toby Dylan Hocking <toby.hocking@r-project.org>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #23 from tdhock/fix-memory-access\n\nfix memory access issue",
    "time": 1733342935
  },
  "_maintainer": {
    "name": "Toby Dylan Hocking",
    "email": "toby.hocking@r-project.org",
    "login": "tdhock",
    "description": "",
    "uuid": 932850
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.14",
      "role": "Depends"
    },
    {
      "package": "PeakError",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "penaltyLearning",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.0",
      "role": "Suggests"
    },
    {
      "package": "microbenchmark",
      "role": "Suggests"
    }
  ],
  "_owner": "tdhock",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 5,
  "_contributors": [
    {
      "user": "tdhock",
      "count": 585,
      "uuid": 932850
    },
    {
      "user": "olifog",
      "count": 1,
      "uuid": 11770524
    }
  ],
  "_userbio": {
    "uuid": 932850,
    "type": "user",
    "name": "Toby Dylan Hocking",
    "followers": 420
  },
  "_downloads": {
    "count": 556,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PeakSegJoint"
  },
  "_devurl": "https://github.com/tdhock/peaksegjoint",
  "_searchresults": 67,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PeakSegJoint.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tdhock/peaksegjoint",
  "_realowner": "tdhock",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2017.08.11",
      "date": "2017-08-15"
    },
    {
      "version": "2018.01.09",
      "date": "2018-10-01"
    },
    {
      "version": "2018.10.3",
      "date": "2018-10-03"
    },
    {
      "version": "2022.4.6",
      "date": "2022-04-07"
    },
    {
      "version": "2023.4.24",
      "date": "2023-04-25"
    },
    {
      "version": "2024.1.24",
      "date": "2024-01-24"
    },
    {
      "version": "2024.6.27",
      "date": "2024-06-27"
    },
    {
      "version": "2024.10.1",
      "date": "2024-10-02"
    },
    {
      "version": "2024.12.4",
      "date": "2024-12-04"
    }
  ],
  "_exports": [
    "binSum",
    "clusterPeaks",
    "ConvertModelList",
    "featureMatrixJoint",
    "multiClusterPeaks",
    "PeakErrorSamples",
    "PeakSegJointError",
    "PeakSegJointFaster",
    "PeakSegJointFasterOne",
    "PeakSegJointHeuristic",
    "PeakSegJointHeuristicStep1",
    "PeakSegJointHeuristicStep2",
    "PeakSegJointSeveral",
    "PoissonLoss",
    "ProfileList"
  ],
  "_datasets": [
    {
      "name": "chr7.peaks",
      "title": "chr7 peaks",
      "object": "chr7.peaks",
      "file": "chr7.peaks.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd"
      ],
      "rows": 41,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo.profiles",
      "title": "Demo profiles",
      "object": "demo.profiles",
      "file": "demo.profiles.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "sample.group",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 51204,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K27ac.TDH.MMM4",
      "title": "Some histone ChIP-seq data",
      "object": "H3K27ac.TDH.MMM4",
      "file": "H3K27ac.TDH.MMM4.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chrom",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 29905,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K36me3.AM.immune.chunk21",
      "title": "H3K36me3_AM_immune chunk 21",
      "object": "H3K36me3.AM.immune.chunk21",
      "file": "H3K36me3.AM.immune.chunk21.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 198142,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K36me3.TDH.other.chunk1",
      "title": "H3K36me3 TDH other chunk 1",
      "object": "H3K36me3.TDH.other.chunk1",
      "file": "H3K36me3.TDH.other.chunk1.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "H3K4me3.PGP.immune.chunk2",
      "title": "H3K4me3 PGP immune chunk 2",
      "object": "H3K4me3.PGP.immune.chunk2",
      "file": "H3K4me3.PGP.immune.chunk2.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 36760,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K4me3.TDH.other.chunk8",
      "title": "H3K4me3_TDH_other chunk 8 subset",
      "object": "H3K4me3.TDH.other.chunk8",
      "file": "H3K4me3.TDH.other.chunk8.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 19866,
      "table": true,
      "tojson": true
    },
    {
      "name": "overflow.list",
      "title": "Data set that caused integer overflow",
      "object": "overflow.list",
      "file": "overflow.list.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "peak.at.profile.end",
      "title": "peak at profile end",
      "object": "peak.at.profile.end",
      "file": "peak.at.profile.end.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "peak1.infeasible",
      "title": "data where the PeakSegJoint model with 1 peak is infeasible",
      "object": "peak1.infeasible",
      "file": "peak1.infeasible.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 4800,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "binSum",
      "title": "binSum",
      "topics": [
        "binSum"
      ]
    },
    {
      "page": "chr7.peaks",
      "title": "chr7 peaks",
      "topics": [
        "chr7.peaks"
      ]
    },
    {
      "page": "clusterPeaks",
      "title": "clusterPeaks",
      "topics": [
        "clusterPeaks"
      ]
    },
    {
      "page": "ConvertModelList",
      "title": "ConvertModelList",
      "topics": [
        "ConvertModelList"
      ]
    },
    {
      "page": "demo.profiles",
      "title": "Demo profiles",
      "topics": [
        "demo.profiles"
      ]
    },
    {
      "page": "featureMatrixJoint",
      "title": "featureMatrixJoint",
      "topics": [
        "featureMatrixJoint"
      ]
    },
    {
      "page": "GeomTallRect",
      "title": "GeomTallRect",
      "topics": [
        "GeomTallRect"
      ]
    },
    {
      "page": "H3K27ac.TDH.MMM4",
      "title": "Some histone ChIP-seq data",
      "topics": [
        "H3K27ac.TDH.MMM4"
      ]
    },
    {
      "page": "H3K36me3.AM.immune.chunk21",
      "title": "H3K36me3_AM_immune chunk 21",
      "topics": [
        "H3K36me3.AM.immune.chunk21"
      ]
    },
    {
      "page": "H3K36me3.TDH.other.chunk1",
      "title": "H3K36me3 TDH other chunk 1",
      "topics": [
        "H3K36me3.TDH.other.chunk1"
      ]
    },
    {
      "page": "H3K4me3.PGP.immune.chunk2",
      "title": "H3K4me3 PGP immune chunk 2",
      "topics": [
        "H3K4me3.PGP.immune.chunk2"
      ]
    },
    {
      "page": "H3K4me3.TDH.other.chunk8",
      "title": "H3K4me3_TDH_other chunk 8 subset",
      "topics": [
        "H3K4me3.TDH.other.chunk8"
      ]
    },
    {
      "page": "multiClusterPeaks",
      "title": "multiClusterPeaks",
      "topics": [
        "multiClusterPeaks"
      ]
    },
    {
      "page": "overflow.list",
      "title": "Data set that caused integer overflow",
      "topics": [
        "overflow.list"
      ]
    },
    {
      "page": "peak.at.profile.end",
      "title": "peak at profile end",
      "topics": [
        "peak.at.profile.end"
      ]
    },
    {
      "page": "peak1.infeasible",
      "title": "data where the PeakSegJoint model with 1 peak is infeasible",
      "topics": [
        "peak1.infeasible"
      ]
    },
    {
      "page": "PeakErrorSamples",
      "title": "PeakErrorSamples",
      "topics": [
        "PeakErrorSamples"
      ]
    },
    {
      "page": "PeakSegJointError",
      "title": "PeakSegJointError",
      "topics": [
        "PeakSegJointError"
      ]
    },
    {
      "page": "PeakSegJointFaster",
      "title": "PeakSegJointFaster",
      "topics": [
        "PeakSegJointFaster"
      ]
    },
    {
      "page": "PeakSegJointFasterOne",
      "title": "PeakSegJointFasterOne",
      "topics": [
        "PeakSegJointFasterOne"
      ]
    },
    {
      "page": "PeakSegJointHeuristic",
      "title": "PeakSegJointHeuristic",
      "topics": [
        "PeakSegJointHeuristic"
      ]
    },
    {
      "page": "PeakSegJointHeuristicStep1",
      "title": "PeakSegJointHeuristicStep1",
      "topics": [
        "PeakSegJointHeuristicStep1"
      ]
    },
    {
      "page": "PeakSegJointHeuristicStep2",
      "title": "PeakSegJointHeuristicStep2",
      "topics": [
        "PeakSegJointHeuristicStep2"
      ]
    },
    {
      "page": "PeakSegJointSeveral",
      "title": "PeakSegJointSeveral",
      "topics": [
        "PeakSegJointSeveral"
      ]
    },
    {
      "page": "PoissonLoss",
      "title": "PoissonLoss",
      "topics": [
        "PoissonLoss"
      ]
    },
    {
      "page": "ProfileList",
      "title": "ProfileList",
      "topics": [
        "ProfileList"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "data.table",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "PeakError",
    "penaltyLearning",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3.525044807036845,
  "_indexed": true,
  "_nocasepkg": "peaksegjoint",
  "_universes": [
    "tdhock"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:11.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/a35432acb6b99c366c77ef92d1b36b84ea361c00dd4eb75588e6a363c06724b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/5e8aa6f8fd5848290b8d278a8d22b4cbe819bf3eebb5a886c3b302f03e0f32c3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:20.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/61c0a4e2e58e893b31ce3e2a5f5054df5a654c1cfb79f103898a2d0f24490f0c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:01.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/60777cf61e442962013d2b239ddd101f8b3af8d0c110b66eec85c6c9980a8797",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.12.4",
      "date": "2026-07-18T07:40:33.000Z",
      "arch": "aarch64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/34f1566fde6d475ae85586cae22c79dd90e18c83e4d58521c45de93289ffd48f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:33.000Z",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/f45d7971e80eb68cb2ebae50f1b46bf25567d5cada7b57803e10e6b21c3cd6d3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2024.12.4",
      "date": "2026-07-18T07:40:31.000Z",
      "arch": "aarch64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/94b95aac5022a70df723e603331847964dc6fa2417be0e151674ad4e35d7eaa3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2024.12.4",
      "date": "2026-07-18T07:41:08.000Z",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/2247995e8606ac8c28f1f2ed2b4eb945fc945e36a36778506119989ecc5752c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2024.12.4",
      "date": "2026-07-18T07:40:48.000Z",
      "arch": "emscripten",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/e2e031743db56c3a0c188be3e23c1b3562e6d6dacf48da8a03a5490e11582241",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2024.12.4",
      "date": "2026-07-18T07:39:59.000Z",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/350c38369989a8151d60f01b046812c8f62a7d2b70eceb841e7b17582270d088",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2024.12.4",
      "date": "2026-07-18T07:40:16.000Z",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/9dc23c86d1301b363a50a9d03aa5882f876cc8f791f530805fb897cf14342a64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2024.12.4",
      "date": "2026-07-18T07:40:01.000Z",
      "arch": "x86_64",
      "commit": "4d094840d3c8172409bb3af440e33d72ebbeac57",
      "fileid": "https://r2.ropensci.org/956378ad6a127c3c1a63c2b32d850f3924f619037fd620d3d1a08569e2c6a79e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/29636012228"
    }
  ]
}