{
  "_id": "6a22aafa0ef520ea2f58b621",
  "Package": "scquantum",
  "Title": "Estimate Ploidy and Absolute Copy Number from Single Cell\nSequencing",
  "Version": "1.0.0",
  "Authors@R": "c(\nperson(given = \"Alexander\",\nfamily = \"Davis\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alexlovesmolecules@gmail.com\"),\nperson(given = \"Taylor\",\nfamily = \"Arnold\",\nrole = \"cph\",\ncomment = \"Author of segmentation function\"),\nperson(given = \"Veeranjaneyulu\",\nfamily = \"Sadhanala\",\nrole = \"cph\",\ncomment = \"Author of segmentation function\"),\nperson(given = \"Ryan\",\nfamily = \"Tibshirani\",\nrole = \"cph\",\ncomment = \"Author of segmentation function\"))",
  "Description": "Given bincount data from single-cell copy number profiling\n(segmented or unsegmented), estimates ploidy, and uses the\nploidy estimate to scale the data to absolute copy numbers.\nUses the modular quantogram proposed by Kendall (1986)\n<doi:10.1002/0471667196.ess2129.pub2>, modified by weighting\nsegments according to confidence, and quantifying confidence in\nthe estimate using a theoretical quantogram. Includes optional\nfused-lasso segmentation with the algorithm in Johnson (2013)\n<doi:10.1080/10618600.2012.681238>, using the implementation\nfrom glmgen by Arnold, Sadhanala, and Tibshirani.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.2",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-05 10:51:32 UTC",
    "User": "root"
  },
  "Author": "Alexander Davis [aut, cre], Taylor Arnold [cph] (Author of\nsegmentation function), Veeranjaneyulu Sadhanala [cph] (Author\nof segmentation function), Ryan Tibshirani [cph] (Author of\nsegmentation function)",
  "Maintainer": "Alexander Davis <alexlovesmolecules@gmail.com>",
  "Repository": "https://alex-l-m.r-universe.dev",
  "Date/Publication": "2022-03-23 08:00:06 UTC",
  "RemoteUrl": "https://github.com/cran/scquantum",
  "RemoteRef": "HEAD",
  "RemoteSha": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
  "MD5sum": "1dd7ccd5279893a5400429856645e6fe",
  "_user": "alex-l-m",
  "_type": "src",
  "_file": "scquantum_1.0.0.tar.gz",
  "_fileid": "34f8d9679c328afa155b142a59f1c3288737d7bd6a2a5a6351e7257ae41262f0",
  "_filesize": 89226,
  "_sha256": "34f8d9679c328afa155b142a59f1c3288737d7bd6a2a5a6351e7257ae41262f0",
  "_created": "2026-06-05T10:51:32.000Z",
  "_published": "2026-06-05T10:54:50.354Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79713167978,
      "time": 104,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7434830618"
    },
    {
      "job": 79713167747,
      "time": 100,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7434828715"
    },
    {
      "job": 79713167869,
      "time": 103,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434830474"
    },
    {
      "job": 79713167913,
      "time": 105,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434830023"
    },
    {
      "job": 79713167995,
      "time": 78,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7434822630"
    },
    {
      "job": 79713167901,
      "time": 137,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7434838668"
    },
    {
      "job": 79713167835,
      "time": 107,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434830800"
    },
    {
      "job": 79713167903,
      "time": 167,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434847343"
    },
    {
      "job": 79712880813,
      "time": 122,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434800992"
    },
    {
      "job": 79713167811,
      "time": 84,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434824494"
    },
    {
      "job": 79713167738,
      "time": 71,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7434821081"
    },
    {
      "job": 79713167772,
      "time": 62,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7434818570"
    },
    {
      "job": 79713167797,
      "time": 67,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7434819837"
    }
  ],
  "_buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/scquantum",
  "_commit": {
    "id": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
    "author": "Alexander Davis <alexlovesmolecules@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.0\n",
    "time": 1648022406
  },
  "_maintainer": {
    "name": "Alexander Davis",
    "email": "alexlovesmolecules@gmail.com",
    "login": "alex-l-m",
    "description": "",
    "uuid": 35587576
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "alex-l-m",
      "count": 1,
      "uuid": 35587576
    }
  ],
  "_userbio": {
    "uuid": 35587576,
    "type": "user",
    "name": "Alexander Davis"
  },
  "_downloads": {
    "count": 154,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scquantum"
  },
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/scquantum.html",
    "manual.pdf"
  ],
  "_realowner": "alex-l-m",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-03-23"
    }
  ],
  "_exports": [
    "ecf.global.max",
    "expected.peak.heights",
    "gat",
    "irises.pluspurple",
    "l2e.normal.sd",
    "ploidy.inference",
    "prof2invals",
    "quantum.sd",
    "seg2invals",
    "segment.summarize",
    "tf.dp",
    "timeseries.iod",
    "weighted.ecf"
  ],
  "_help": [
    {
      "page": "ploidy.inference",
      "title": "Ploidy inference with quantogram",
      "topics": [
        "ploidy.inference"
      ]
    }
  ],
  "_readme": "https://github.com/cran/scquantum/raw/HEAD/README.md",
  "_rundeps": [],
  "_score": 1.9542425094393248,
  "_indexed": true,
  "_nocasepkg": "scquantum",
  "_universes": [
    "alex-l-m"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:25.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "9aa0a90b73e22ce5e076d10f772e5ff40c34a3eb7060b23c432a9410e37e6de4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:16.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "137443b0af7d897b38d21fa3db72c581cef2bb1ab481a2139f723e663f16f457",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:22.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "3b19bf0efd6916d1f9fbbb8841c977a5b8795946bf11c1691b38e93aca3055bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "1a48905707f06b533c4515e52f2a151c49884fdfe60680955df1d16c585bf78a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-05T10:52:53.000Z",
      "arch": "aarch64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "2a5dfae3d0c0425eaada1c3151191f122cb5126ff5a32b5af07e88ae1e805b0c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:44.000Z",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "466c5686d34a523331e0ee4f9133d6ccd0b932fce4a8c4448127122339766024",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:20.000Z",
      "arch": "aarch64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "2cf8c65485ce7be13fb3d80ad33bccfb980797bafbcee6faa835d7bf0800054f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-05T10:54:15.000Z",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "4fa97a76bc843af067707889e7467ea95b5ce3e0fca59d6d65fe9dfaa16dd3fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-06-05T10:53:08.000Z",
      "arch": "emscripten",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "63cdde58a4b7dfb3c85f4dfa2fee633a91cad1df91a68bc34b2c443d9eb03bb2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-05T10:52:37.000Z",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "44bba2f147efb1ac0845a857bd1c1d3e76f3868ffe215ef4b09dd58a6f3d8e5e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-05T10:52:28.000Z",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "295d6a62cd0750653e69a0175b87954799c6dad86c94c5049170c92965785e79",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-05T10:52:34.000Z",
      "arch": "x86_64",
      "commit": "b6fcd39eeffd807e2a89587fd391b0d5e58af196",
      "fileid": "194506e8fdc67f963211ebc6dc9d47f33d02149109ee8b03908bed00acc492d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alex-l-m/actions/runs/27010562205"
    }
  ]
}