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  "Title": "IP-seq data analysis and vizualization",
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  "Date": "2025-07-22",
  "Authors@R": "c(\nperson(\"Matthias\", \"Lienhard\", role=c(\"aut\", \"cre\"), email=\"lienhard@molgen.mpg.de\", comment = c(ORCID = \"0000-0002-2549-3142\")),\nperson(\"Lukas\", \"Chavez\", role=\"aut\", comment = c(ORCID = \"0000-0002-8718-8848\")),\nperson(\"Ralf\", \"Herwig\", role=\"aut\", comment = c(ORCID = \"0000-0002-9335-1760\")))",
  "Description": "qsea (quantitative sequencing enrichment analysis) was\ndeveloped as the successor of the MEDIPS package for analyzing\ndata derived from methylated DNA immunoprecipitation (MeDIP)\nexperiments followed by sequencing (MeDIP-seq). However, qsea\nprovides several functionalities for the analysis of other\nkinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq,\nCMS-seq and others) including calculation of differential\nenrichment between groups of samples.",
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      "page": "qsea-package",
      "title": "QSEA: Quantitative sequencing enrichment analysis and visualization",
      "topics": [
        "qsea-package",
        "QSEA",
        "qsea"
      ]
    },
    {
      "page": "addCNV",
      "title": "estimate CNV information and add to qseaSet object",
      "topics": [
        "addCNV"
      ]
    },
    {
      "page": "addContrast",
      "title": "fit GLMs to reduced model and test for significance",
      "topics": [
        "addContrast"
      ]
    },
    {
      "page": "addCoverage",
      "title": "Import sequencing data",
      "topics": [
        "addCoverage"
      ]
    },
    {
      "page": "addEnrichmentParameters",
      "title": "Enrichment analysis",
      "topics": [
        "addEnrichmentParameters"
      ]
    },
    {
      "page": "addLibraryFactors",
      "title": "Estimate effective library size",
      "topics": [
        "addLibraryFactors"
      ]
    },
    {
      "page": "addNewSamples",
      "title": "Extends an exisiting qseaSet by new samples",
      "topics": [
        "addNewSamples"
      ]
    },
    {
      "page": "addOffset",
      "title": "Estimate background reads",
      "topics": [
        "addOffset"
      ]
    },
    {
      "page": "addPatternDensity",
      "title": "Infer sequence pattern density values and add to qseaSet object",
      "topics": [
        "addPatternDensity"
      ]
    },
    {
      "page": "addSeqPref",
      "title": "Add sequence preference to qseaSet object",
      "topics": [
        "addSeqPref"
      ]
    },
    {
      "page": "createQseaSet",
      "title": "Prepares a qseaSet Object",
      "topics": [
        "createQseaSet"
      ]
    },
    {
      "page": "fitNBglm",
      "title": "Fit GLM for each window",
      "topics": [
        "fitNBglm"
      ]
    },
    {
      "page": "example",
      "title": "Simulation of MeDIP seq QSEA set",
      "topics": [
        "getExampleQseaSet"
      ]
    },
    {
      "page": "getPCA",
      "title": "Principle Component Analysis (PCA) in QSea",
      "topics": [
        "getPCA"
      ]
    },
    {
      "page": "isSignificant",
      "title": "Finds Significant Regions",
      "topics": [
        "isSignificant"
      ]
    },
    {
      "page": "makeTable",
      "title": "Create a Results Table",
      "topics": [
        "makeTable"
      ]
    },
    {
      "page": "normMethod",
      "title": "Definition of normalization procedure",
      "topics": [
        "normMethod"
      ]
    },
    {
      "page": "plotCNV",
      "title": "Plots a Heatmap-like Overview of the CNVs",
      "topics": [
        "plotCNV"
      ]
    },
    {
      "page": "plotCoverage",
      "title": "Plots a genome-browser-like image of a region",
      "topics": [
        "plotCoverage"
      ]
    },
    {
      "page": "plotEnrichmentProfile",
      "title": "Plotting functions for enrichment profiles",
      "topics": [
        "plotEnrichmentProfile",
        "plotEPmatrix"
      ]
    },
    {
      "page": "plotPCA",
      "title": "Plots for Principle Component Analysis (PCA) in QSEA",
      "topics": [
        "plotPCA",
        "plotPCA,qseaPCA-method",
        "plotPCAfactors",
        "plotPCAfactors,qseaPCA-method"
      ]
    },
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      "title": "qseaGLM class and its methods",
      "topics": [
        "addParameters,qseaGLM-method",
        "getParameters,qseaGLM-method",
        "getSampleNames,qseaGLM-method",
        "qseaGLM",
        "qseaGLM-class",
        "show,qseaGLM-method"
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      "title": "qseaPCA class and its methods",
      "topics": [
        "getSampleNames,qseaPCA-method",
        "qseaPCA",
        "qseaPCA-class",
        "show,qseaPCA-method"
      ]
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      "title": "qseaSet class and its methods",
      "topics": [
        "addParameters,qseaSet-method",
        "getChrNames",
        "getChrNames,qseaSet-method",
        "getCNV",
        "getCNV,qseaSet-method",
        "getCounts",
        "getCounts,qseaSet-method",
        "getLibSize",
        "getLibSize,qseaSet-method",
        "getNormFactors",
        "getNormFactors,qseaSet-method",
        "getOffset",
        "getOffset,qseaSet-method",
        "getParameters",
        "getParameters,qseaSet-method",
        "getRegions",
        "getRegions,qseaSet-method",
        "getSampleGroups",
        "getSampleGroups,qseaSet-method",
        "getSampleNames",
        "getSampleNames,qseaSet-method",
        "getSampleTable",
        "getSampleTable,qseaSet-method",
        "getWindowSize",
        "getWindowSize,qseaSet-method",
        "getZygosity",
        "getZygosity,qseaSet-method",
        "hasCNV",
        "hasCNV,qseaSet-method",
        "qseaSet",
        "qseaSet-class",
        "setZygosity",
        "setZygosity,qseaSet-method",
        "show,qseaSet-method"
      ]
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    {
      "page": "regionStats",
      "title": "Counts the Windows in Regions of Interest",
      "topics": [
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      ]
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