{
  "_id": "6ad336872c5c76d3dd0c9eb9",
  "Package": "MethylMix",
  "Title": "MethylMix: Identifying methylation driven cancer genes",
  "Version": "2.43.0",
  "Description": "MethylMix is an algorithm implemented to identify hyper\nand hypomethylated genes for a disease. MethylMix is based on a\nbeta mixture model to identify methylation states and compares\nthem with the normal DNA methylation state. MethylMix uses a\nnovel statistic, the Differential Methylation value or DM-value\ndefined as the difference of a methylation state with the\nnormal methylation state. Finally, matched gene expression data\nis used to identify, besides differential, functional\nmethylation states by focusing on methylation changes that\neffect gene expression. References: Gevaert 0. MethylMix: an R\npackage for identifying DNA methylation-driven genes.\nBioinformatics (Oxford, England). 2015;31(11):1839-41.\ndoi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R,\nPlevritis SK. Pancancer analysis of DNA methylation-driven\ngenes using MethylMix. Genome Biology. 2015;16(1):17.\ndoi:10.1186/s13059-014-0579-8.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Author": "Olivier Gevaert",
  "Maintainer": "Olivier Gevaert <olivier.gevaert@gmail.com>",
  "Type": "Package",
  "Date": "2018-07-13",
  "biocViews": "DNAMethylation,StatisticalMethod,DifferentialMethylation,GeneRegulation,GeneExpression,MethylationArray,DifferentialExpression,Pathways,Network",
  "RoxygenNote": "6.0.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:39 UTC",
  "RemoteUrl": "https://github.com/bioc/MethylMix",
  "RemoteRef": "HEAD",
  "RemoteSha": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 08:40:47 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "MethylMix_2.43.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b17c75e63c232af6a84747060d2f34d599846128624a72b7d7a6fd076b802fcb",
  "_filesize": 2829823,
  "_sha256": "b17c75e63c232af6a84747060d2f34d599846128624a72b7d7a6fd076b802fcb",
  "_expires": "2027-01-25T08:49:00.000Z",
  "_created": "2026-10-17T08:40:47.000Z",
  "_published": "2026-10-17T08:49:10.933Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 14
  },
  "_upstream": "https://github.com/bioc/MethylMix",
  "_commit": {
    "id": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
    "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": 1777379979
  },
  "_maintainer": {
    "name": "Olivier Gevaert",
    "email": "olivier.gevaert@gmail.com",
    "login": "ogevaert",
    "description": "",
    "uuid": 23532631
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117354810109,
      "time": 147,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12095656709"
    },
    {
      "job": 117354810130,
      "time": 268,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12095698053"
    },
    {
      "job": 117354810180,
      "time": 269,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12096170575"
    },
    {
      "job": 117354810178,
      "time": 129,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12095887360"
    },
    {
      "job": 117354810141,
      "time": 135,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12095871357"
    },
    {
      "job": 117354208520,
      "time": 197,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12095289573"
    },
    {
      "job": 117354810128,
      "time": 95,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12095812130"
    },
    {
      "job": 117354810210,
      "time": 158,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12095737719"
    },
    {
      "job": 117354810200,
      "time": 175,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12095991282"
    },
    {
      "job": 117354810146,
      "time": 164,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12096100543"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.0",
      "role": "Depends"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "RPMM",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "R.matlab",
      "role": "Imports"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.43.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "2.42.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "dnamethylation",
    "statisticalmethod",
    "differentialmethylation",
    "generegulation",
    "geneexpression",
    "methylationarray",
    "differentialexpression",
    "pathways",
    "network"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 696,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MethylMix"
  },
  "_mentions": 53,
  "_searchresults": 38,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MethylMix.html",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ClusterProbes",
    "Download_DNAmethylation",
    "Download_GeneExpression",
    "GetData",
    "MethylMix",
    "MethylMix_ModelGeneExpression",
    "MethylMix_PlotModel",
    "MethylMix_Predict",
    "Preprocess_DNAmethylation",
    "Preprocess_GeneExpression"
  ],
  "_datasets": [
    {
      "name": "BatchData",
      "title": "BatchData data set",
      "object": "BatchData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ArrayName",
        "SampleName",
        "Batch"
      ],
      "rows": 23263,
      "table": true,
      "tojson": true
    },
    {
      "name": "GEcancer",
      "title": "Cancer Gene expression data of glioblastoma patients from the TCGA project",
      "object": "GEcancer",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
      "name": "METcancer",
      "title": "DNA methylation data from cancer tissue from glioblastoma patients from the TCGA project",
      "object": "METcancer",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
      "name": "METnormal",
      "title": "DNA methylation data from normal tissue from glioblastoma patients",
      "object": "METnormal",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "X4321207019_B",
        "X4321207026_C",
        "X4321207042_E",
        "X4321207042_K"
      ],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
      "name": "ProbeAnnotation",
      "title": "ProbeAnnotation data set",
      "object": "ProbeAnnotation",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ILMNID",
        "GENESYMBOL"
      ],
      "rows": 365860,
      "table": true,
      "tojson": true
    },
    {
      "name": "SNPprobes",
      "title": "SNPprobes data set",
      "object": "SNPprobes",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BatchData",
      "title": "BatchData data set",
      "topics": [
        "BatchData"
      ]
    },
    {
      "page": "ClusterProbes",
      "title": "The ClusterProbes function",
      "topics": [
        "ClusterProbes"
      ]
    },
    {
      "page": "Download_DNAmethylation",
      "title": "The Download_DNAmethylation function",
      "topics": [
        "Download_DNAmethylation"
      ]
    },
    {
      "page": "Download_GeneExpression",
      "title": "The Download_GeneExpression function",
      "topics": [
        "Download_GeneExpression"
      ]
    },
    {
      "page": "GEcancer",
      "title": "Cancer Gene expression data of glioblastoma patients from the TCGA project",
      "topics": [
        "GEcancer"
      ]
    },
    {
      "page": "GetData",
      "title": "The GetData function",
      "topics": [
        "GetData"
      ]
    },
    {
      "page": "METcancer",
      "title": "DNA methylation data from cancer tissue from glioblastoma patients from the TCGA project",
      "topics": [
        "METcancer"
      ]
    },
    {
      "page": "MethylMix",
      "title": "MethylMix: Mixture model for DNA methylation data in cancer.",
      "topics": [
        "MethylMix"
      ]
    },
    {
      "page": "MethylMix_ModelGeneExpression",
      "title": "The MethylMix_ModelGeneExpression function",
      "topics": [
        "MethylMix_ModelGeneExpression"
      ]
    },
    {
      "page": "MethylMix_PlotModel",
      "title": "The MethylMix_PlotModel function.",
      "topics": [
        "MethylMix_PlotModel"
      ]
    },
    {
      "page": "MethylMix_Predict",
      "title": "The MethylMix_Predict function",
      "topics": [
        "MethylMix_Predict"
      ]
    },
    {
      "page": "METnormal",
      "title": "DNA methylation data from normal tissue from glioblastoma patients",
      "topics": [
        "METnormal"
      ]
    },
    {
      "page": "predictOneGene",
      "title": "The predictOneGene function",
      "topics": [
        "predictOneGene"
      ]
    },
    {
      "page": "Preprocess_DNAmethylation",
      "title": "The Preprocess_DNAmethylation function",
      "topics": [
        "Preprocess_DNAmethylation"
      ]
    },
    {
      "page": "Preprocess_GeneExpression",
      "title": "The Preprocess_GeneExpression function",
      "topics": [
        "Preprocess_GeneExpression"
      ]
    },
    {
      "page": "ProbeAnnotation",
      "title": "ProbeAnnotation data set",
      "topics": [
        "ProbeAnnotation"
      ]
    },
    {
      "page": "SNPprobes",
      "title": "SNPprobes data set",
      "topics": [
        "SNPprobes"
      ]
    }
  ],
  "_rundeps": [
    "bitops",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "data.table",
    "digest",
    "farver",
    "foreach",
    "ggplot2",
    "glue",
    "gtable",
    "impute",
    "isoband",
    "iterators",
    "labeling",
    "lifecycle",
    "limma",
    "R.matlab",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "RCurl",
    "rlang",
    "RPMM",
    "S7",
    "scales",
    "statmod",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "vignettes.Rmd",
      "filename": "vignettes.html",
      "title": "MethylMix",
      "author": "| Olivier Gevaert | | Stanford Center for Biomedical Informatics | Department of Medicine | 1265 Welch Road | Stanford CA, 94305-5479",
      "engine": "knitr::rmarkdown",
      "headings": [
        "4. Data input for MethylMix",
        "5. Running MethylMix",
        "6. Graphical output",
        "7. References",
        "8. Sesssion Info"
      ],
      "created": "2017-01-14 03:16:03",
      "modified": "2018-08-30 17:52:07",
      "commits": 5
    }
  ],
  "_score": 5.357934847000454,
  "_indexed": true,
  "_nocasepkg": "methylmix",
  "_universes": [
    "bioc",
    "ogevaert"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.43.0",
      "date": "2026-10-17T08:44:22.000Z",
      "distro": "resolute",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/174bd3ed82e92fd07f2e6f83d920d21140821298889d694e3309f72e1e0bd946",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.43.0",
      "date": "2026-10-17T08:44:36.000Z",
      "distro": "resolute",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/0a9fbea20f14c1ffec62f8d9ac5281090c31dab9371e3be605a76ab996ce294f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.43.0",
      "date": "2026-10-17T08:47:52.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/024bfcb8b78539aae6cb515834ad207824916061f38f30adfd3a6cf41854b77c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.43.0",
      "date": "2026-10-17T08:47:09.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/87bceaa0b29c23847c7247f6a064da961d5299d55a7e9f43f0655a0dbd380334",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.43.0",
      "date": "2026-10-17T08:42:46.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/68f7314cf9269854e0e9b77eb59a12e1c8105bd577dc3945a19fc9b46696b457",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-10-17T08:42:11.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/8dab4ae6e3a5fb770507d056a34761ed748fef207b096f66eb6b506bc8c43b60",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-10-17T08:42:10.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/9bd0a81fdec997af511a7bc8ac19aade501880950dafb58918fff9870eb6a751",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-10-17T08:42:00.000Z",
      "commit": "2a9a439bfbe5719f23e41993379ef6b51ff456be",
      "fileid": "https://r2.ropensci.org/85717f30b602a45c8dbc2e67d46b67e47e332766b3e280b0f98972f7621a220b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39018067813"
    }
  ]
}