{
  "_id": "6a2bac375783985943194e0e",
  "Package": "methInheritSim",
  "Type": "Package",
  "Title": "Simulating Whole-Genome Inherited Bisulphite Sequencing Data",
  "Description": "Simulate a multigeneration methylation case versus control\nexperiment with inheritance relation using a real control\ndataset.",
  "Version": "1.34.0",
  "Date": "2025-07-22",
  "Author": "Pascal Belleau, Astrid Deschênes and Arnaud Droit",
  "Author@R": "c(person(\"Pascal\", \"Belleau\",\nemail=\"pascal_belleau@hotmail.com\", role=c(\"cre\", \"aut\")),\nperson(\"Astrid\", \"Deschênes\", email=\"adeschen@hotmail.com\",\nrole=c(\"aut\")), person(\"Arnaud\", \"Droit\",\nemail=\"arnaud.droit@crchuq.ulaval.ca\", role=c(\"aut\")))",
  "Encoding": "UTF-8",
  "License": "Artistic-2.0",
  "URL": "https://github.com/belleau/methInheritSim",
  "BugReports": "https://github.com/belleau/methInheritSim/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "BiologicalQuestion, Epigenetics, DNAMethylation,\nDifferentialMethylation, MethylSeq, Software, ImmunoOncology,\nStatisticalMethod, WholeGenome, Sequencing",
  "Maintainer": "Pascal Belleau <pascal_belleau@hotmail.com>",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:44 UTC",
  "RemoteUrl": "https://github.com/bioc/methInheritSim",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-12 06:42:15 UTC",
    "User": "root"
  },
  "MD5sum": "54c66f784b0eab123760a9287cc8ea1d",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "methInheritSim_1.34.0.tar.gz",
  "_fileid": "a9752de9d92d9987e8fd309c522c6669aa9c6dfe7c985cadf0758c754467ad2a",
  "_filesize": 1074296,
  "_sha256": "a9752de9d92d9987e8fd309c522c6669aa9c6dfe7c985cadf0758c754467ad2a",
  "_created": "2026-06-12T06:42:15.000Z",
  "_published": "2026-06-12T06:50:31.761Z",
  "_jobs": [
    {
      "job": 80973813250,
      "time": 217,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7584903727"
    },
    {
      "job": 80973813249,
      "time": 407,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7584955182"
    },
    {
      "job": 80973813240,
      "time": 430,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7584961005"
    },
    {
      "job": 80973813241,
      "time": 292,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7584923687"
    },
    {
      "job": 80973813238,
      "time": 272,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7584917035"
    },
    {
      "job": 80973180136,
      "time": 283,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7584845192"
    },
    {
      "job": 80973813222,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7584883934"
    },
    {
      "job": 80973813233,
      "time": 403,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7584955268"
    },
    {
      "job": 80973813243,
      "time": 317,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7584930757"
    },
    {
      "job": 80973813246,
      "time": 380,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7584947291"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/methInheritSim",
  "_commit": {
    "id": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380344
  },
  "_maintainer": {
    "name": "Pascal Belleau",
    "email": "pascal_belleau@hotmail.com",
    "login": "belleau",
    "description": "Computational Postdoctoral Fellow",
    "uuid": 8398253
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methylKit",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "msm",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "methylInheritance",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "biologicalquestion",
    "epigenetics",
    "dnamethylation",
    "differentialmethylation",
    "methylseq",
    "software",
    "immunooncology",
    "statisticalmethod",
    "wholegenome",
    "sequencing",
    "bisulphite-sequencing",
    "inheritance",
    "methylation",
    "simulation"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "adeschen",
      "count": 230,
      "uuid": 7254636
    },
    {
      "user": "belleau",
      "count": 122,
      "uuid": 8398253
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 348,
    "source": "https://www.bioconductor.org/packages/stats/bioc/methInheritSim"
  },
  "_devurl": "https://github.com/belleau/methinheritsim",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/methInheritSim.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/belleau/methinheritsim",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "runSim"
  ],
  "_datasets": [
    {
      "name": "dataSimExample",
      "title": "A 'list' containing methylation information used by some internal functions (for demo purpose.",
      "object": "dataSimExample",
      "file": "dataSimExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "samplesForChrSynthetic",
      "title": "All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).",
      "object": "samplesForChrSynthetic",
      "file": "samplesForChrSynthetic.RData",
      "class": [
        "methylBase"
      ],
      "fields": [
        "chr",
        "start",
        "end",
        "strand",
        "coverage1",
        "numCs1",
        "numTs1",
        "coverage2",
        "numCs2",
        "numTs2",
        "coverage3",
        "numCs3",
        "numTs3",
        "coverage4",
        "numCs4",
        "numTs4",
        "coverage5",
        "numCs5",
        "numTs5",
        "coverage6",
        "numCs6",
        "numTs6",
        "coverage7",
        "numCs7",
        "numTs7",
        "coverage8",
        "numCs8",
        "numTs8",
        "coverage9",
        "numCs9",
        "numTs9",
        "coverage10",
        "numCs10",
        "numTs10",
        "coverage11",
        "numCs11",
        "numTs11",
        "coverage12",
        "numCs12",
        "numTs12"
      ],
      "rows": 9864,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "methInheritSim-package",
      "title": "methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data",
      "topics": [
        "methInheritSim-package",
        "methInheritSim"
      ]
    },
    {
      "page": "dataSimExample",
      "title": "A 'list' containing methylation information used by some internal functions (for demo purpose.",
      "topics": [
        "dataSimExample"
      ]
    },
    {
      "page": "runSim",
      "title": "Simulate a multigeneration methylation experiment with inheritance",
      "topics": [
        "runSim"
      ]
    },
    {
      "page": "samplesForChrSynthetic",
      "title": "All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).",
      "topics": [
        "samplesForChrSynthetic"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/methInheritSim/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "bbmle",
    "bdsmatrix",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "cli",
    "coda",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DelayedArray",
    "emdbook",
    "expm",
    "farver",
    "fastseg",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "methylKit",
    "mgcv",
    "mime",
    "msm",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "qvalue",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "methInheritSim.Rmd",
      "filename": "methInheritSim.html",
      "title": "Simulating Whole-Genome Inherited Bisulphite Sequencing Data",
      "author": "Pascal Belleau, Astrid Deschênes and Arnaud Droit",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Licensing",
        "Citing",
        "Introduction",
        "Loading methInheritSim package",
        "Description of the simulation process",
        "Simulated control dataset",
        "Simulated case dataset",
        "Case study",
        "The simulated dataset",
        "The simulation",
        "Files generated by the simulation",
        "Synthetic chromosome in GRanges format (\"syntheticChr\" prefix)",
        "Simulation information in GRanges format (\"simData\" prefix)",
        "Information about DMS state (\"stateDiff\" prefix)",
        "Files related to saveGRanges parameter",
        "Raw methylation data for all samples in GRanges format (\"methylGR\" prefix)",
        "Information about controls and cases (\"treatment\" prefix)",
        "Files related to saveMethylKit parameter",
        "Raw methylation data in methylRaw format (\"methylObj\" prefix)",
        "Files related to runAnalysis parameter",
        "Methylation events present in multiple samples in methylBase format (\"meth\" prefix)",
        "Differential methylation statistics in methylDiff format (\"methDiff\" prefix)",
        "Conclusion"
      ],
      "created": "2017-03-30 12:29:38",
      "modified": "2018-09-29 21:16:52",
      "commits": 5
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": false,
  "_nocasepkg": "methinheritsim",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/methInheritSim",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-06-12T06:45:55.000Z",
      "distro": "noble",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "510cbb6540d774b3d76dfd97e1c322def4ac1b8a19dcfbe55a95feb06fc33d80",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-06-12T06:46:07.000Z",
      "distro": "noble",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "1ad077978e51dca5b7b95564815fc53b20dbb6645e9099208b46f26af0133ac0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-06-12T06:45:16.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "e9a60d31f4ba95a1f2c92637f8915838863ba597189bc2b35df3de0f24acb075",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-06-12T06:44:21.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "ebc179d33a45fa376f58cdffbbc0b12717750bd84c3183f094895454e6adb997",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.34.0",
      "date": "2026-06-12T06:45:18.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "059daaa301e076a620ada4bc38ed07bcab19f36c1ad217102a746c6b4655c17b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-12T06:44:57.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "dc90fb2e3baff3292b0dd99164abfde642822cc518ab097d1cf46deb5f50123f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-12T06:44:18.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "c3c81ac820432a37bd39ce6c12cfe4e7953fb58c849efd5f87737d4e9ffe7b77",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-06-12T06:44:17.000Z",
      "commit": "675d5f21aa6f52b236a719cedf55cc465dd6054e",
      "fileid": "77b16c3f15e1fb2af315c7417e3e41ccc0d044ecb697747ac3c1874d8102a5cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27399223999"
    }
  ]
}