{
  "_id": "6a195dc5acfb0bcc41de4c3e",
  "Package": "Clomial",
  "Type": "Package",
  "Title": "Infers clonal composition of a tumor",
  "Version": "1.49.0",
  "Date": "2018-05-31",
  "Author": "Habil Zare and Alex Hu",
  "Maintainer": "Habil Zare <zare@u.washington.edu>",
  "Description": "Clomial fits binomial distributions to counts obtained\nfrom Next Gen Sequencing data of multiple samples of the same\ntumor. The trained parameters can be interpreted to infer the\nclonal structure of the tumor.",
  "License": "GPL (>= 2)",
  "biocViews": "Genetics, GeneticVariability, Sequencing, Clustering,\nMultipleComparison, Bayesian, DNASeq, ExomeSeq,\nTargetedResequencing, ImmunoOncology",
  "LazyLoad": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:42 UTC",
  "RemoteUrl": "https://github.com/bioc/Clomial",
  "RemoteRef": "HEAD",
  "RemoteSha": "ca3ec4d09c62e776f17f5636e27a4671de335643",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:13:03 UTC",
    "User": "root"
  },
  "MD5sum": "fe350efdf34492b8e3284526886f2c47",
  "_user": "bioc",
  "_type": "src",
  "_file": "Clomial_1.49.0.tar.gz",
  "_fileid": "81c5ea626bf82b2162b12717c7a3dc4efcbdf651c1c49270fa64b866471048fb",
  "_filesize": 1546878,
  "_sha256": "81c5ea626bf82b2162b12717c7a3dc4efcbdf651c1c49270fa64b866471048fb",
  "_created": "2026-05-29T08:13:03.000Z",
  "_published": "2026-05-29T09:35:01.191Z",
  "_jobs": [
    {
      "job": 78463385983,
      "time": 127,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7286191471"
    },
    {
      "job": 78463385921,
      "time": 221,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286217791"
    },
    {
      "job": 78463386033,
      "time": 179,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286205905"
    },
    {
      "job": 78463386024,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7287627869"
    },
    {
      "job": 78463385967,
      "time": 95,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7287609380"
    },
    {
      "job": 78463007687,
      "time": 158,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286155029"
    },
    {
      "job": 78463385963,
      "time": 89,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286180979"
    },
    {
      "job": 78463385985,
      "time": 213,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286216025"
    },
    {
      "job": 78463385992,
      "time": 152,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286198460"
    },
    {
      "job": 78463385989,
      "time": 189,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286209251"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Clomial",
  "_commit": {
    "id": "ca3ec4d09c62e776f17f5636e27a4671de335643",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379922
  },
  "_maintainer": {
    "name": "Habil Zare",
    "email": "zare@u.washington.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "matrixStats",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "permute",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "geneticvariability",
    "sequencing",
    "clustering",
    "multiplecomparison",
    "bayesian",
    "dnaseq",
    "exomeseq",
    "targetedresequencing",
    "immunooncology"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 396,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Clomial"
  },
  "_mentions": 10,
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/Clomial.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "choose.best",
    "Clomial",
    "Clomial.generate.data",
    "Clomial.iterate",
    "Clomial.likelihood",
    "compute.bic",
    "compute.errors"
  ],
  "_datasets": [
    {
      "name": "breastCancer",
      "title": "Breast cancer data for clonal decomposition.",
      "object": "breastCancer",
      "file": "breastCancer.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Clomial1000",
      "title": "Pre-computed results of Clomial.",
      "object": "Clomial1000",
      "file": "Clomial1000.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "Clomial-package",
      "title": "Fits a binomial model to data from multiple samples of a single tumor to infer its clonal decomposition.",
      "topics": [
        "Clomial-package"
      ]
    },
    {
      "page": "breastCancer",
      "title": "Breast cancer data for clonal decomposition.",
      "topics": [
        "breastCancer"
      ]
    },
    {
      "page": "choose.best",
      "title": "Chooses the best trained Clomial model.",
      "topics": [
        "choose.best"
      ]
    },
    {
      "page": "Clomial",
      "title": "Fits several binomial models to data from multiple samples of a single tumor.",
      "topics": [
        "Clomial"
      ]
    },
    {
      "page": "Clomial.generate.data",
      "title": "Generates simulated data to test performance of Clomial algorithm.",
      "topics": [
        "Clomial.generate.data"
      ]
    },
    {
      "page": "Clomial.iterate",
      "title": "Runs EM iterations until convergence of the Clomial model.",
      "topics": [
        "Clomial.iterate"
      ]
    },
    {
      "page": "Clomial.likelihood",
      "title": "Computes the complete data log-likelihood of a Clomial model.",
      "topics": [
        "Clomial.likelihood"
      ]
    },
    {
      "page": "Clomial1000",
      "title": "Pre-computed results of Clomial.",
      "topics": [
        "Clomial1000"
      ]
    },
    {
      "page": "compute.bic",
      "title": "Computes BIC for a Clomial model.",
      "topics": [
        "compute.bic"
      ]
    },
    {
      "page": "compute.errors",
      "title": "Computes the error of a Clomial model.",
      "topics": [
        "compute.errors"
      ]
    }
  ],
  "_rundeps": [
    "matrixStats",
    "permute"
  ],
  "_vignettes": [
    {
      "source": "Clonal_decomposition_by_Clomial.Rnw",
      "filename": "Clonal_decomposition_by_Clomial.pdf",
      "title": "A likelihood maximization approach to infer the clonal structure of a cancer using multiple tumor samples",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-03-10 20:31:51",
      "modified": "2021-02-10 17:02:51",
      "commits": 7
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "clomial",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-05-29T08:16:11.000Z",
      "distro": "noble",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "46593265d7e85b6d1576bb3f0f9586b84effd3425dbdfdf12362a38fc0be682d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-05-29T08:15:12.000Z",
      "distro": "noble",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "51d7c4591f0d96c075e6df645ed7da03bf0e59b4ddf0614774096ed7b30029cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-05-29T09:34:08.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "f72732ff0d0957cd69e0c6fb346ab87a92ea7acde02c203432e997679d007016",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-05-29T09:33:08.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "704439ca7c82556906c25260d180d9c157282fea271dd85bb05d92b6510e9ae5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.49.0",
      "date": "2026-05-29T08:14:48.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "350ef50c4ef881908fd53270da4ba3760dc3c5b50f74363485717c326040a7e7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-05-29T08:14:51.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "5ded1a3c15782db82a9947a26832ffede6208ac46d4cbd643ae5a5d269233714",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-05-29T08:14:24.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "9b62ea95234511dc454548d976d5cecad1a6bf2a11f4c63246f5430ec50cd4f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-05-29T08:14:38.000Z",
      "commit": "ca3ec4d09c62e776f17f5636e27a4671de335643",
      "fileid": "f9ec9bb3088cdf0a9cd1cffd03e064009dec9651ed7118a63bbb2dc2e171f25a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626055274"
    }
  ]
}