{
  "_id": "6ae33e6d327abcdf86866faa",
  "Package": "CNORdt",
  "Type": "Package",
  "Title": "Add-on to CellNOptR: Discretized time treatments",
  "Version": "1.55.0",
  "Date": "2012-09-18",
  "Author": "A. MacNamara",
  "Maintainer": "A. MacNamara <aidan.macnamara@ebi.ac.uk>",
  "Description": "This add-on to the package CellNOptR handles time-course\ndata, as opposed to steady state data in CellNOptR. It scales\nthe simulation step to allow comparison and model fitting for\ntime-course data. Future versions will optimize delays and\nstrengths for each edge.",
  "License": "GPL-2",
  "LazyLoad": "yes",
  "biocViews": "ImmunoOncology, CellBasedAssays, CellBiology, Proteomics,\nTimeCourse",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:57 UTC",
  "RemoteUrl": "https://github.com/bioc/CNORdt",
  "RemoteRef": "HEAD",
  "RemoteSha": "b36db97fe53d27b821cea03001733228923337ef",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-29 11:32:41 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "CNORdt_1.55.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6043805e3c7360342586d04cac916f0f43ccc5c4a268eebf1bc244ef28ae17a1",
  "_filesize": 319827,
  "_sha256": "6043805e3c7360342586d04cac916f0f43ccc5c4a268eebf1bc244ef28ae17a1",
  "_expires": "2027-02-06T12:39:07.000Z",
  "_created": "2026-10-29T11:32:41.000Z",
  "_published": "2026-10-29T12:39:09.354Z",
  "_upstream": "https://github.com/bioc/CNORdt",
  "_status": "success",
  "_maintainer": {
    "name": "A. MacNamara",
    "email": "aidan.macnamara@ebi.ac.uk"
  },
  "_jobs": [
    {
      "job": 123421640713,
      "time": 138,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12894495514"
    },
    {
      "job": 123421640704,
      "time": 183,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12894092075"
    },
    {
      "job": 123421640799,
      "time": 324,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12894515770"
    },
    {
      "job": 123421640765,
      "time": 183,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12893497778"
    },
    {
      "job": 123421640715,
      "time": 291,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12893722878"
    },
    {
      "job": 123421640720,
      "time": 155,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12897561693"
    },
    {
      "job": 123421640653,
      "time": 335,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12896774458"
    },
    {
      "job": 123421640794,
      "time": 181,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12897945751"
    },
    {
      "job": 123421640896,
      "time": 371,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12897941258"
    },
    {
      "job": 123418928887,
      "time": 376,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12894096521"
    },
    {
      "job": 123421640605,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12893942351"
    },
    {
      "job": 123421640655,
      "time": 279,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12894176978"
    },
    {
      "job": 123421640681,
      "time": 219,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12893942593"
    },
    {
      "job": 123421640946,
      "time": 153,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12894605332"
    },
    {
      "job": 123421640667,
      "time": 295,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12894042436"
    },
    {
      "job": 123421640725,
      "time": 181,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12893239614"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458",
  "_commit": {
    "id": "b36db97fe53d27b821cea03001733228923337ef",
    "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": 1777379817
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 1.8.0",
      "role": "Depends"
    },
    {
      "package": "CellNOptR",
      "version": ">= 0.99",
      "role": "Depends"
    },
    {
      "package": "abind",
      "role": "Depends"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "cellbasedassays",
    "cellbiology",
    "proteomics",
    "timecourse"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 494,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CNORdt"
  },
  "_mentions": 2,
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNORdt.html",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "computeScoreDT",
    "convert2array",
    "cutAndPlotResultsDT",
    "gaBinaryDT",
    "getFitDT",
    "simulatorDT"
  ],
  "_datasets": [
    {
      "name": "CNOlistPB",
      "title": "Toy data",
      "object": "CNOlistPB",
      "file": "CNOlistPB.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "modelPB",
      "title": "modelPB",
      "object": "modelPB",
      "file": "modelPB.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CNOlistPB",
      "title": "Toy data",
      "topics": [
        "CNOlistPB"
      ]
    },
    {
      "page": "computeScoreDT",
      "title": "Compute the score of a model/data (time-course) set using a bitString to cut the model.",
      "topics": [
        "computeScoreDT"
      ]
    },
    {
      "page": "convert2array",
      "title": "Converts the output of simulatorDT to a 3D array for other functions",
      "topics": [
        "convert2array"
      ]
    },
    {
      "page": "cutAndPlotResultsDT",
      "title": "Plot the results of a time-course optimization",
      "topics": [
        "cutAndPlotResultsDT"
      ]
    },
    {
      "page": "gaBinaryDT",
      "title": "Genetic algorithm for optimizing models using multiple time-points",
      "topics": [
        "gaBinaryDT"
      ]
    },
    {
      "page": "getFitDT",
      "title": "The optimization function that finds the scaling factor for the boolean simulation",
      "topics": [
        "getFitDT"
      ]
    },
    {
      "page": "modelPB",
      "title": "modelPB",
      "topics": [
        "modelPB"
      ]
    },
    {
      "page": "simulatorDT",
      "title": "Discrete time simulation of a boolean model",
      "topics": [
        "simulatorDT"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "base64enc",
    "BH",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "CellNOptR",
    "cli",
    "cpp11",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "graph",
    "gtable",
    "highr",
    "htmltools",
    "igraph",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "pkgconfig",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "RCurl",
    "Rgraphviz",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CNORdt-vignette.Rnw",
      "filename": "CNORdt-vignette.pdf",
      "title": "Using multiple time points to train logic models to data",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:27:15",
      "modified": "2018-08-30 17:46:23",
      "commits": 2
    }
  ],
  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "cnordt",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:34:40.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/bfb4d4d660f50fa95a570dc8eceb3c291a6e11eac0338bd7d355cf911c1437fb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:36:42.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/d4921753c97d58df58ee738561e7773ffaf1df2af260d5995139e991a2cf1bc4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:34:42.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/af910b7d1fefd7f3230d35ef30a51dac6586d9b0b3c705bbab54350e40620b00",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:36:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/7d6295f4ce17928b156143d26a260e4e8ba245bc83e1b199594d74ab42304e60",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:31:33.000Z",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/201b31c302cae9db7f9d49aac0d70df5bd069a681b03b2db321b62462cfa1733",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:35:14.000Z",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/880100f11bbbe0e70d2df1976992530ff0da42599f9dd71385373a159e7539dc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:31:56.000Z",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/dab50df5d75f3b1f17acfd8b70d3de9ea0ba8941793e96ec4c4b28857ec43259",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:36:12.000Z",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/d241f32311a71affa2aa8988e364ca898732ec68531865faed75b674238b004f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.55.0",
      "date": "2026-10-29T11:35:12.000Z",
      "arch": "emscripten",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/81b1c5db24eba4561c2a5999087922f244eb7d9c073d9b0647cf5b64aba4d65f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:35:53.000Z",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/b4a92591aec035ce87b9483423ff5acfa5318e22fac2ae0223ace2b3744d6b2f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:34:15.000Z",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/33138fc545a0955ead77f2c3a49c8ba7bea2728b3e849ae8bfeacd0ef880e129",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:33:58.000Z",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/9a47078f7ff1570a85e79d8385045a1cd92858e633dcd1f572584d2cf9469c01",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:36:13.000Z",
      "arch": "aarch64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/2e15bd5e2fe205434fab83181020258dbc202b67c28035062cf67f3247fce27c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:34:13.000Z",
      "arch": "x86_64",
      "commit": "b36db97fe53d27b821cea03001733228923337ef",
      "fileid": "https://r2.ropensci.org/685129c3a7d4b4d962d1a5e4f3c8c04b995f3f81915910251890cba62c0ed922",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40865409458"
    }
  ]
}