{
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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.",
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  "Date/Publication": "2026-04-28 12:34:58 UTC",
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    "differentialexpression",
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    "preprocessing",
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  "_exports": [
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    "bin.ROIs",
    "chr_lengths",
    "chr_names",
    "extend",
    "genome_CF",
    "genome_count",
    "genome_name",
    "getGRange",
    "getMObjectFromWIG",
    "getPairedGRange",
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    "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"
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  "_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"
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    },
    {
      "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"
      ]
    }
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      "source": "MEDIPS.Rnw",
      "filename": "MEDIPS.pdf",
      "title": "MEDIPS",
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      "headings": [
        "1 Introduction",
        "2 Installation",
        "3 Preparations",
        "4 Case study: Genome wide methylation and differential coverage between two conditions",
        "5 Quality controls",
        "6 Miscellaneous"
      ],
      "created": "2013-11-01 20:15:46",
      "modified": "2018-08-30 17:51:47",
      "commits": 9
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