{
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  "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",
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  "Date/Publication": "2026-04-28 12:34:58 UTC",
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  "_created": "2026-07-05T00:07:37.000Z",
  "_published": "2026-07-05T00:16:57.243Z",
  "_bioccheck": {
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    "warning": 5,
    "note": 18
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722712282",
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  "_upstream": "https://github.com/bioc/MEDIPS",
  "_commit": {
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    "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
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    "name": "Lukas Chavez",
    "email": "lukaschavez@ucsd.edu",
    "login": "lukaschavez",
    "description": "",
    "uuid": 41491954
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      "role": "Suggests"
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    "cpgisland",
    "differentialexpression",
    "sequencing",
    "chipseq",
    "preprocessing",
    "qualitycontrol",
    "visualization",
    "microarray",
    "genetics",
    "coverage",
    "genomeannotation",
    "copynumbervariation",
    "sequencematching"
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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    "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",
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        "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"
      ]
    }
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      "os": "win",
      "version": "1.65.0",
      "date": "2026-07-05T00:10:30.000Z",
      "commit": "ffde1fc53565794733a17fa30837d021fe36caf6",
      "fileid": "https://r2.ropensci.org/eca77d09e1e11ffa7574bae49b9b55e6d4989d6b3079a016e27817733bb40139",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722712282"
    }
  ]
}