{
  "_id": "6a1ac11b1d7bb097a09d795f",
  "Package": "nucleoSim",
  "Version": "1.41.0",
  "Date": "2015-07-24",
  "Title": "Generate synthetic nucleosome maps",
  "Description": "This package can generate a synthetic map with reads\ncovering the nucleosome regions as well as a synthetic map with\nforward and reverse reads emulating next-generation sequencing.\nThe synthetic hybridization data of “Tiling Arrays” can also be\ngenerated. The user has choice between three different\ndistributions for the read positioning: Normal, Student and\nUniform. In addition, a visualization tool is provided to\nexplore the synthetic nucleosome maps.",
  "Encoding": "UTF-8",
  "Authors@R": "c(person(\"Rawane\", \"Samb\",\nemail=\"rawane.samb.1@ulaval.ca\", role=c(\"aut\")),\nperson(\"Astrid\", \"Deschênes\",\nemail=\"adeschen@hotmail.com\",\nrole=c(\"cre\",\"aut\"), comment = c(ORCID = \"0000-0001-7846-6749\")),\nperson(\"Pascal\", \"Belleau\",\nemail=\"pascal_belleau@hotmail.com\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-0802-1071\")),\nperson(\"Arnaud\", \"Droit\",\nemail=\"arnaud.droit@crchuq.ulaval.ca\", role=c(\"aut\")))",
  "License": "Artistic-2.0",
  "URL": "https://github.com/arnauddroitlab/nucleoSim",
  "BugReports": "https://github.com/arnauddroitlab/nucleoSim/issues",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "biocViews": "Genetics, Sequencing, Software, StatisticalMethod, Alignment",
  "RoxygenNote": "7.1.2",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:53 UTC",
  "RemoteUrl": "https://github.com/bioc/nucleoSim",
  "RemoteRef": "HEAD",
  "RemoteSha": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
  "Packaged": {
    "Date": "2026-05-30 07:22:37 UTC",
    "User": "root"
  },
  "Author": "Rawane Samb [aut],\nAstrid Deschênes [cre, aut] (ORCID:\n<https://orcid.org/0000-0001-7846-6749>),\nPascal Belleau [aut] (ORCID: <https://orcid.org/0000-0002-0802-1071>),\nArnaud Droit [aut]",
  "Maintainer": "Astrid Deschênes <adeschen@hotmail.com>",
  "MD5sum": "1632aead32d9340b5e4e0793c956aaa9",
  "_user": "bioc",
  "_type": "src",
  "_file": "nucleoSim_1.41.0.tar.gz",
  "_fileid": "cc5e4abe4ff0c185f0525fd419add1e7b2b59adfcccf51189b2d8f4a6270d94f",
  "_filesize": 364195,
  "_sha256": "cc5e4abe4ff0c185f0525fd419add1e7b2b59adfcccf51189b2d8f4a6270d94f",
  "_created": "2026-05-30T07:22:37.000Z",
  "_published": "2026-05-30T10:51:07.243Z",
  "_jobs": [
    {
      "job": 78633212359,
      "time": 144,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306446691"
    },
    {
      "job": 78633212370,
      "time": 192,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306452386"
    },
    {
      "job": 78633212372,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306447348"
    },
    {
      "job": 78633212377,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307559389"
    },
    {
      "job": 78633212375,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307561473"
    },
    {
      "job": 78633050514,
      "time": 181,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306430975"
    },
    {
      "job": 78633212374,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306442181"
    },
    {
      "job": 78633212381,
      "time": 92,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306441092"
    },
    {
      "job": 78633212390,
      "time": 89,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306440562"
    },
    {
      "job": 78633212405,
      "time": 95,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306441270"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/nucleoSim",
  "_commit": {
    "id": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
    "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": 1777380173
  },
  "_maintainer": {
    "name": "Astrid Deschênes",
    "email": "adeschen@hotmail.com",
    "login": "adeschen",
    "orcid": "0000-0001-7846-6749",
    "description": "I am a Computational Science Analyst at Cold Spring Harbor Laboratory. ",
    "uuid": 7254636
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "sequencing",
    "software",
    "statisticalmethod",
    "alignment",
    "bioconductor",
    "nucleosome-maps",
    "nucleosomes",
    "simulation",
    "simulator",
    "synthetic-nucleosomes"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "adeschen",
      "count": 149,
      "uuid": 7254636
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "hpages",
      "count": 4,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 4,
      "uuid": 2466173
    },
    {
      "user": "belleau",
      "count": 1,
      "uuid": 8398253
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 373,
    "source": "https://www.bioconductor.org/packages/stats/bioc/nucleoSim"
  },
  "_devurl": "https://github.com/arnauddroitlab/nucleosim",
  "_searchresults": 16,
  "_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/nucleoSim.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/arnauddroitlab/nucleosim",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "syntheticNucMapFromDist",
    "syntheticNucReadsFromDist",
    "syntheticNucReadsFromMap"
  ],
  "_help": [
    {
      "page": "nucleoSim-package",
      "title": "nucleoSim: Generate synthetic nucleosome maps",
      "topics": [
        "nucleoSim-package",
        "nucleoSim"
      ]
    },
    {
      "page": "plot.syntheticNucMap",
      "title": "Generate a graph of a synthetic nucleosome map",
      "topics": [
        "plot.syntheticNucMap"
      ]
    },
    {
      "page": "plot.syntheticNucReads",
      "title": "Generate a graph of a synthetic nucleosome map containing forward and reverse reads",
      "topics": [
        "plot.syntheticNucReads"
      ]
    },
    {
      "page": "syntheticNucMapFromDist",
      "title": "Generate a synthetic nucleosome map containing complete sequences",
      "topics": [
        "syntheticNucMapFromDist"
      ]
    },
    {
      "page": "syntheticNucReadsFromDist",
      "title": "Generate a synthetic nucleosome map containing forward and reverse reads (paired-end reads)",
      "topics": [
        "syntheticNucReadsFromDist"
      ]
    },
    {
      "page": "syntheticNucReadsFromMap",
      "title": "Generate a synthetic nucleosome map containing forward and reverse reads",
      "topics": [
        "syntheticNucReadsFromMap"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/nucleoSim/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "IRanges",
    "S4Vectors"
  ],
  "_vignettes": [
    {
      "source": "nucleoSim.Rmd",
      "filename": "nucleoSim.html",
      "title": "Generate synthetic nucleosome maps",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Licensing and citing",
        "Introduction",
        "Loading r Rpackage(\"nucleoSim\") package",
        "Description",
        "Synthetic Nucleosome Maps",
        "Create a nucleosome map using syntheticNucMapFromDist()",
        "Simulate hybridization data of Tiling Arrays",
        "Synthetic Nucleosome Samples",
        "Create a nucleosome sample using syntheticNucReadsFromDist()",
        "Create a nucleosome sample using syntheticNucReadsFromMap()",
        "Session info"
      ],
      "created": "2016-03-06 08:27:26",
      "modified": "2017-09-06 22:06:04",
      "commits": 3
    }
  ],
  "_score": 5.204119982655925,
  "_indexed": true,
  "_nocasepkg": "nucleosim",
  "_universes": [
    "bioc",
    "adeschen",
    "arnauddroitlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T07:25:32.000Z",
      "distro": "noble",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "8da62577b2045641955281decebce42422fb92e72aa96db347ee4c390a01a351",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T07:24:55.000Z",
      "distro": "noble",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "c4da83c018c6b16f1933e482160226f7d1ae0b862e46b7e6eefc84d7fdf764e9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T10:36:18.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "4b4036f3fecf119ff9fb05e628dc65cc3ab4ee2ac5efcb4683d1499014643edd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T10:36:33.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "8ad9545964a018a39f654871ab788630a169908b8a66fa0f92d52dea2f360b04",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-05-30T07:24:42.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "227d4d298ad87615a2ddf5c84972e15f2c73ca02330f888fa84d1fb03dfeeaf9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T07:23:53.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "3b132777a70190d0956991cbcf339592a6d4485b49eb5f18844bed77fdd9d563",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T07:23:49.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "1e3b66d7cd5b0b69f664cd7cf66ce664bc85b09d2f665d116d1aeaa259a62e6b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T07:23:54.000Z",
      "commit": "0d9bca7dc45cb0072490f3316a737767f6767b2b",
      "fileid": "050ab7139cdc9e645ee73f6f719288d95182a69ce4102dd365902051eba2c387",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677900502"
    }
  ]
}