{
  "_id": "6a49975d74ff1be5edd7932c",
  "Package": "MEDME",
  "Type": "Package",
  "Title": "Modelling Experimental Data from MeDIP Enrichment",
  "Version": "1.73.0",
  "Date": "2009-3-26",
  "Author": "Mattia Pelizzola and Annette Molinaro",
  "Description": "MEDME allows the prediction of absolute and relative\nmethylation levels based on measures obtained by\nMeDIP-microarray experiments",
  "Maintainer": "Mattia Pelizzola <mattia.pelizzola@gmail.com>",
  "License": "GPL (>= 2)",
  "LazyLoad": "yes",
  "biocViews": "Microarray, CpGIsland, DNAMethylation",
  "Config/pak/sysreqs": "cmake make libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:11 UTC",
  "RemoteUrl": "https://github.com/bioc/MEDME",
  "RemoteRef": "HEAD",
  "RemoteSha": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 23:17:58 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "MEDME_1.73.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/2700939fdeb1f23138e6aee905fa724a470921c52282ba7497243bca3827a017",
  "_filesize": 458342,
  "_sha256": "2700939fdeb1f23138e6aee905fa724a470921c52282ba7497243bca3827a017",
  "_expires": "2026-10-12T23:29:31.000Z",
  "_created": "2026-07-04T23:17:58.000Z",
  "_published": "2026-07-04T23:29:33.046Z",
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077",
  "_status": "success",
  "_upstream": "https://github.com/bioc/MEDME",
  "_commit": {
    "id": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
    "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": 1777379591
  },
  "_maintainer": {
    "name": "Mattia Pelizzola",
    "email": "mattia.pelizzola@gmail.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85175081213,
      "time": 263,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8086339002"
    },
    {
      "job": 85175081266,
      "time": 300,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086343181"
    },
    {
      "job": 85175081250,
      "time": 358,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086348642"
    },
    {
      "job": 85175081253,
      "time": 311,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086344242"
    },
    {
      "job": 85175081248,
      "time": 354,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086348264"
    },
    {
      "job": 85175081264,
      "time": 218,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086351551"
    },
    {
      "job": 85175081245,
      "time": 324,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086348350"
    },
    {
      "job": 85175081255,
      "time": 220,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086351718"
    },
    {
      "job": 85175081244,
      "time": 407,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086355109"
    },
    {
      "job": 85174772455,
      "time": 330,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086311095"
    },
    {
      "job": 85175081205,
      "time": 279,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8086340568"
    },
    {
      "job": 85175081243,
      "time": 622,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086378127"
    },
    {
      "job": 85175081252,
      "time": 631,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086378891"
    },
    {
      "job": 85175081242,
      "time": 654,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086381214"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.15",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "drc",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg18",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm9",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.73.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.72.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "cpgisland",
    "dnamethylation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 20,
  "_searchresults": 3,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MEDME.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AMS",
    "CG",
    "CGcount",
    "chr",
    "initialize",
    "logR",
    "MEDME",
    "MEDME.predict",
    "MEDME.readFiles",
    "MEDME.writeFiles",
    "org",
    "pos",
    "RMS",
    "show",
    "smooth",
    "smoothed"
  ],
  "_datasets": [
    {
      "name": "testMEDMEset",
      "title": "Dataset of class MEDMEset for testing MEDME",
      "object": "testMEDMEset",
      "file": "testMEDMEset.rda",
      "class": [
        "MEDMEset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "CGcount",
      "title": "Determining the count of CpG dinucleotides for a set of genomic locations",
      "topics": [
        "CGcount"
      ]
    },
    {
      "page": "MEDME",
      "title": "Determining the logistic model of MeDIP enrichment in respect to the expected DNA methylation level",
      "topics": [
        "MEDME"
      ]
    },
    {
      "page": "MEDME.predict",
      "title": "Applying the logistic model on MeDIP enrichment data",
      "topics": [
        "MEDME.predict"
      ]
    },
    {
      "page": "MEDME.readFiles",
      "title": "reading sgr or gff files for MEDME",
      "topics": [
        "MEDME.readFiles"
      ]
    },
    {
      "page": "MEDME.writeFiles",
      "title": "writeFiles sgr or gff files from MEDME output",
      "topics": [
        "MEDME.writeFiles"
      ]
    },
    {
      "page": "MEDMEset-class",
      "title": "Class \"MEDMEset\"",
      "topics": [
        "AMS",
        "AMS,MEDMEset-method",
        "CG",
        "CG,MEDMEset-method",
        "CGcounts",
        "chr",
        "chr,MEDMEset-method",
        "initialize,MEDMEset-method",
        "logR",
        "logR,MEDMEset-method",
        "MEDMEset-class",
        "org",
        "org,MEDMEset-method",
        "organism",
        "pos",
        "pos,MEDMEset-method",
        "RMS",
        "RMS,MEDMEset-method",
        "show,MEDMEset-method",
        "smoothed",
        "smoothed,MEDMEset-method",
        "[,MEDMEset-method"
      ]
    },
    {
      "page": "smooth",
      "title": "Determining weighted MeDIP data",
      "topics": [
        "smooth"
      ]
    },
    {
      "page": "testMEDMEset",
      "title": "Dataset of class MEDMEset for testing MEDME",
      "topics": [
        "testMEDMEset"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "backports",
    "BiocGenerics",
    "Biostrings",
    "boot",
    "broom",
    "car",
    "carData",
    "cli",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "crayon",
    "Deriv",
    "doBy",
    "dplyr",
    "drc",
    "farver",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "minqa",
    "modelr",
    "multcomp",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plotrix",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "S4Vectors",
    "S7",
    "sandwich",
    "scales",
    "Seqinfo",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "TH.data",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "MEDME.rnw",
      "filename": "MEDME.pdf",
      "title": "MEDME",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:05:21",
      "modified": "2013-11-01 20:05:21",
      "commits": 1
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "medme",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/06b8b4393c981d6c8c733b1c0c05ee2baf2f3dc7d09c601593e0477fc3db707b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:49.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/f95f576056ded81c458c4460bc94dca766f4a0d90fa58dec56f57561ab17a71b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:29.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/d5d447c5f59d518fd5fa7de4bad4a5fd82b3d3a8a0be57f41239b357f1b630d6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:47.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/6cc076719db73a9a593bbe5f9c4db1bbe2cdf698cd6b1fafc6352d6fc5fb2cd8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-04T23:23:31.000Z",
      "arch": "aarch64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/8386bbf0a6a6b3cbfa1004694066a956bd7e5c704d34416d2badd1e11a3e9291",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:35.000Z",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/8e93c49f27416a5f0fb9a57b8b9979d1a46624541c84f25c058575ecd3acf3ed",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-04T23:23:19.000Z",
      "arch": "aarch64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/cfd91e08dbcc36fe2f404300941cbb9f4b06437c29073123990b85f6be5c693a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-04T23:23:20.000Z",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/5e0f94921f34be6edd36773d51a602a0d590c274900481a597522ec42367ef7f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.73.0",
      "date": "2026-07-04T23:22:56.000Z",
      "arch": "emscripten",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/1762aa351617673fd39d263af973e8d830912512e4015a0734b5972c960b4656",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-04T23:27:06.000Z",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/d973ff47802e9033b8e5a2b7041b8b12132e3bc0bcd3c634014226b73411a1b1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-04T23:27:12.000Z",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/e7bcdd84829c32715454e507adfca6df86206351da38d8555413d4a51e9c8184",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-04T23:27:38.000Z",
      "arch": "x86_64",
      "commit": "626920b4895ea6c9a68f54cd75997f79ff0947bb",
      "fileid": "https://r2.ropensci.org/79b9991cd1db9ef9c96d22e331876d0a45ce619bab4e67357a3b64bccee31f74",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722705077"
    }
  ]
}