{
  "_id": "6a1ac8361d7bb097a09dc08a",
  "Package": "MEDIPS",
  "Type": "Package",
  "Title": "DNA IP-seq data analysis",
  "Version": "1.65.0",
  "Date": "2020-02-15",
  "Author": "Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez\nMoyado",
  "Maintainer": "Lukas Chavez <lukaschavez@ucsd.edu>",
  "Description": "MEDIPS was developed for analyzing data derived from\nmethylated DNA immunoprecipitation (MeDIP) experiments followed\nby sequencing (MeDIP-seq). However, MEDIPS provides\nfunctionalities for the analysis of any kind of quantitative\nsequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others)\nincluding calculation of differential coverage between groups\nof samples and saturation and correlation analysis.",
  "License": "GPL (>=2)",
  "LazyLoad": "yes",
  "biocViews": "DNAMethylation, CpGIsland, DifferentialExpression,\nSequencing, ChIPSeq, Preprocessing, QualityControl,\nVisualization, Microarray, Genetics, Coverage,\nGenomeAnnotation, CopyNumberVariation, SequenceMatching",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:45:50 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:58 UTC",
  "RemoteUrl": "https://github.com/bioc/MEDIPS",
  "RemoteRef": "HEAD",
  "RemoteSha": "ffde1fc53565794733a17fa30837d021fe36caf6",
  "MD5sum": "1e658d28ba7dd3d5586c77dab3e1a227",
  "_user": "bioc",
  "_type": "src",
  "_file": "MEDIPS_1.65.0.tar.gz",
  "_fileid": "3e6a2ac43c63795a8d5adb93730812378ce41b4d45d9af72f2460890438a1fd7",
  "_filesize": 502445,
  "_sha256": "3e6a2ac43c63795a8d5adb93730812378ce41b4d45d9af72f2460890438a1fd7",
  "_created": "2026-05-30T07:45:50.000Z",
  "_published": "2026-05-30T11:21:26.913Z",
  "_jobs": [
    {
      "job": 78634463222,
      "time": 257,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306608329"
    },
    {
      "job": 78634463240,
      "time": 550,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306636949"
    },
    {
      "job": 78634463217,
      "time": 518,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306633700"
    },
    {
      "job": 78634463220,
      "time": 421,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307808684"
    },
    {
      "job": 78634463218,
      "time": 317,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307798078"
    },
    {
      "job": 78634106330,
      "time": 433,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306582860"
    },
    {
      "job": 78634463212,
      "time": 207,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306603299"
    },
    {
      "job": 78634463229,
      "time": 438,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306625974"
    },
    {
      "job": 78634463227,
      "time": 387,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306621019"
    },
    {
      "job": 78634463225,
      "time": 436,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306625863"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 5,
    "note": 19
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MEDIPS",
  "_commit": {
    "id": "ffde1fc53565794733a17fa30837d021fe36caf6",
    "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": 1777379698
  },
  "_maintainer": {
    "name": "Lukas Chavez",
    "email": "lukaschavez@ucsd.edu",
    "login": "lukaschavez",
    "description": "",
    "uuid": 41491954
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Depends"
    },
    {
      "package": "Rsamtools",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "DNAcopy",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "MEDIPSData",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.65.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.64.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dnamethylation",
    "cpgisland",
    "differentialexpression",
    "sequencing",
    "chipseq",
    "preprocessing",
    "qualitycontrol",
    "visualization",
    "microarray",
    "genetics",
    "coverage",
    "genomeannotation",
    "copynumbervariation",
    "sequencematching"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 526,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MEDIPS"
  },
  "_mentions": 89,
  "_searchresults": 99,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MEDIPS.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adjustReads",
    "bin_number",
    "bin.ROIs",
    "chr_lengths",
    "chr_names",
    "extend",
    "genome_CF",
    "genome_count",
    "genome_name",
    "getGRange",
    "getMObjectFromWIG",
    "getPairedGRange",
    "getTypes",
    "matDiff",
    "matMax",
    "matMean",
    "matMin",
    "matNnotNA",
    "matSd",
    "matTtest",
    "MEDIPS.addCNV",
    "MEDIPS.calibrationCurve",
    "MEDIPS.cnv",
    "MEDIPS.correlation",
    "MEDIPS.couplingVector",
    "MEDIPS.CpGenrich",
    "MEDIPS.createROIset",
    "MEDIPS.createSet",
    "MEDIPS.diffMeth",
    "MEDIPS.exportWIG",
    "MEDIPS.GenomicCoordinates",
    "MEDIPS.getAnnotation",
    "MEDIPS.getPositions",
    "MEDIPS.mergeFrames",
    "MEDIPS.mergeSets",
    "MEDIPS.meth",
    "MEDIPS.plotCalibrationPlot",
    "MEDIPS.plotSaturation",
    "MEDIPS.plotSeqCoverage",
    "MEDIPS.rms",
    "MEDIPS.saturation",
    "MEDIPS.selectROIs",
    "MEDIPS.selectSig",
    "MEDIPS.seqCoverage",
    "MEDIPS.setAnnotation",
    "number_pattern",
    "number_regions",
    "path_name",
    "rois",
    "sample_name",
    "scanBamToGRanges",
    "seq_pattern",
    "setTypes",
    "shifted",
    "show",
    "uniq",
    "window_size"
  ],
  "_help": [
    {
      "page": "MEDIPS-package",
      "title": "(MeD)IP-seq data analysis",
      "topics": [
        "MEDIPS-package",
        "MEDIPS"
      ]
    },
    {
      "page": "COUPLINGset-class",
      "title": "COUPLINGset class and internal functions",
      "topics": [
        "chr_lengths,COUPLINGset-method",
        "chr_names,COUPLINGset-method",
        "COUPLINGset",
        "COUPLINGset-class",
        "genome_CF",
        "genome_CF,COUPLINGset-method",
        "genome_name,COUPLINGset-method",
        "number_pattern",
        "number_pattern,COUPLINGset-method",
        "seq_pattern",
        "seq_pattern,COUPLINGset-method",
        "show,COUPLINGset-method",
        "window_size,COUPLINGset-method"
      ]
    },
    {
      "page": "MEDIPS.addCNV",
      "title": "Function to run a copy number variation analysis.",
      "topics": [
        "MEDIPS.addCNV"
      ]
    },
    {
      "page": "MEDIPS.correlation",
      "title": "Calculates pairwise Pearson correlations between provided MEDIPS SETs",
      "topics": [
        "MEDIPS.correlation"
      ]
    },
    {
      "page": "MEDIPS.couplingVector",
      "title": "Calculates the sequence pattern densities at genome wide windows.",
      "topics": [
        "MEDIPS.couplingVector"
      ]
    },
    {
      "page": "MEDIPS.CpGenrich",
      "title": "Calculates CpG enrichment of provided short reads compared to the reference genome.",
      "topics": [
        "MEDIPS.CpGenrich"
      ]
    },
    {
      "page": "MEDIPS.createROIset",
      "title": "Creates a MEDIPS ROI SET by reading a suitable input file",
      "topics": [
        "bin.ROIs",
        "MEDIPS.createROIset"
      ]
    },
    {
      "page": "MEDIPS.createSet",
      "title": "Creates a MEDIPS SET by reading a suitable input file",
      "topics": [
        "getMObjectFromWIG",
        "getPairedGRange",
        "MEDIPS.createSet",
        "readRegionsFile",
        "scanBamToGRanges"
      ]
    },
    {
      "page": "MEDIPS.exportWIG",
      "title": "Exports count, rpkm, or sequence pattern densities into a wiggle file.",
      "topics": [
        "MEDIPS.exportWIG"
      ]
    },
    {
      "page": "MEDIPS.getAnnotation",
      "title": "Funtion to fetch annotations from biomaRt.",
      "topics": [
        "MEDIPS.getAnnotation"
      ]
    },
    {
      "page": "MEDIPS.mergeFrames",
      "title": "Merges genomic coordinates of neighboring windows into one supersized window",
      "topics": [
        "MEDIPS.mergeFrames"
      ]
    },
    {
      "page": "MEDIPS.mergeSets",
      "title": "Creates one merged MEDIPS SET out of two.",
      "topics": [
        "MEDIPS.mergeSets"
      ]
    },
    {
      "page": "MEDIPS.meth",
      "title": "Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable.",
      "topics": [
        "MEDIPS.diffMeth",
        "MEDIPS.meth"
      ]
    },
    {
      "page": "MEDIPS.plotCalibrationPlot",
      "title": "Creates the calibration plot.",
      "topics": [
        "MEDIPS.plotCalibrationPlot"
      ]
    },
    {
      "page": "MEDIPS.plotSaturation",
      "title": "Function plots the results of the MEDIPS.saturationAnalysis function.",
      "topics": [
        "MEDIPS.plotSaturation"
      ]
    },
    {
      "page": "MEDIPS.plotSeqCoverage",
      "title": "Function plots the results of the MEDIPS.seqCoverage function.",
      "topics": [
        "MEDIPS.plotSeqCoverage"
      ]
    },
    {
      "page": "MEDIPS.saturation",
      "title": "Function calculates the saturation/reproducibility of the provided IP-Seq data.",
      "topics": [
        "MEDIPS.saturation"
      ]
    },
    {
      "page": "MEDIPS.selectROIs",
      "title": "Selects row-wise subsets of a result table as returned by the MEDIPS.meth function.",
      "topics": [
        "MEDIPS.selectROIs"
      ]
    },
    {
      "page": "MEDIPS.selectSig",
      "title": "Selects windows which show significant differential coverage between two MEDIPS SETs from a resultTable (as returned by the function MEDIPS.meth).",
      "topics": [
        "MEDIPS.selectSig"
      ]
    },
    {
      "page": "MEDIPS.seqCoverage",
      "title": "The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.",
      "topics": [
        "MEDIPS.seqCoverage"
      ]
    },
    {
      "page": "MEDIPS.setAnnotation",
      "title": "Funtion to annotate a matrix of genomic coordinates (i.e. a result table) by a given annotation object.",
      "topics": [
        "MEDIPS.setAnnotation"
      ]
    },
    {
      "page": "MEDIPSroiSet-class",
      "title": "MEDIPSroiSet class and internal functions",
      "topics": [
        "bin_number",
        "bin_number,MEDIPSroiSet-method",
        "chr_lengths,MEDIPSroiSet-method",
        "chr_names,MEDIPSroiSet-method",
        "extend,MEDIPSroiSet-method",
        "genome_count,MEDIPSroiSet-method",
        "genome_name,MEDIPSroiSet-method",
        "MEDIPSroiSet",
        "MEDIPSroiSet-class",
        "number_regions,MEDIPSroiSet-method",
        "path_name,MEDIPSroiSet-method",
        "ROI,MEDIPSroiSet-method",
        "rois",
        "rois,MEDIPSroiSet-method",
        "sample_name,MEDIPSroiSet-method",
        "shifted,MEDIPSroiSet-method",
        "show,MEDIPSroiSet-method",
        "uniq,MEDIPSroiSet-method"
      ]
    },
    {
      "page": "MEDIPSset-class",
      "title": "MEDIPSset class and internal functions",
      "topics": [
        "adjustReads",
        "bin_size",
        "bin_size,MEDIPSset-method",
        "chr_lengths",
        "chr_lengths,MEDIPSset-method",
        "chr_names",
        "chr_names,MEDIPSset-method",
        "extend",
        "extend,MEDIPSset-method",
        "genome_count",
        "genome_count,MEDIPSset-method",
        "genome_name",
        "genome_name,MEDIPSset-method",
        "getGRange",
        "getTypes",
        "matDiff",
        "matMax",
        "matMean",
        "matMin",
        "matNnotNA",
        "matSd",
        "matTtest",
        "MEDIPS.Bam2GRanges",
        "MEDIPS.Bed2Granges",
        "MEDIPS.calibrationCurve",
        "MEDIPS.cnv",
        "MEDIPS.GenomicCoordinates",
        "MEDIPS.getPositions",
        "MEDIPS.rms",
        "MEDIPSset",
        "MEDIPSset-class",
        "number_regions",
        "number_regions,MEDIPSset-method",
        "path_name",
        "path_name,MEDIPSset-method",
        "sample_name",
        "sample_name,MEDIPSset-method",
        "setTypes",
        "shifted",
        "shifted,MEDIPSset-method",
        "show",
        "show,MEDIPSset-method",
        "uniq",
        "uniq,MEDIPSset-method",
        "window_size",
        "window_size,MEDIPSset-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DNAcopy",
    "dplyr",
    "edgeR",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "glue",
    "gtools",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "MEDIPS.Rnw",
      "filename": "MEDIPS.pdf",
      "title": "MEDIPS",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:15:46",
      "modified": "2018-08-30 17:51:47",
      "commits": 9
    }
  ],
  "_score": 5.7737864449811935,
  "_indexed": true,
  "_nocasepkg": "medips",
  "_universes": [
    "bioc",
    "lukaschavez"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.65.0",
      "date": "2026-05-30T07:51:30.000Z",
      "distro": "noble",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "57fbdf9039ac5ab1cba7275190f48241e4881a9dc9184a08488f5359ddd75dc9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.65.0",
      "date": "2026-05-30T07:51:15.000Z",
      "distro": "noble",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "5633d1318f60524add91141ac23b1520d026b127d7c13137b337d24a6d431e40",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.65.0",
      "date": "2026-05-30T11:16:57.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "95dec9436b92551206db59ac85cf40995cb5b99da2efffcd3f8e65fe17db268b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.65.0",
      "date": "2026-05-30T11:15:55.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "5a20c7b04e87b3b36bcf5ae4d7250532f4beccadbc656f0f22facb640eaa4e11",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.65.0",
      "date": "2026-05-30T07:50:05.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "1817a4cbe30d52168c32f0efbf4d841e1f294564a5a3006dbd75f79c594aefcc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.65.0",
      "date": "2026-05-30T07:49:00.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "1ebefedcd581deb3d2c0086e231ac69facd502c3bdbd0151af9f4847b0a91151",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.65.0",
      "date": "2026-05-30T07:48:46.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "830d73dc05350ee18ba9fc55f9b19f5b501791480dbec9784e5f33ca44fc59af",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.65.0",
      "date": "2026-05-30T07:48:54.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "6a36c0b283d892a2f3e91f81b2da1c6048166c3e6b93f2f43124387e6e9ff466",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678282785"
    }
  ]
}