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      "title": "MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)",
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        "mosaics"
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        "tagCount",
        "tagCount,BinData-method"
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    {
      "page": "constructBins",
      "title": "Construct bin-level ChIP-sep data from an aligned read file",
      "topics": [
        "constructBins"
      ]
    },
    {
      "page": "estimates",
      "title": "Extract estimates of the fitted MOSAiCS model",
      "topics": [
        "estimates",
        "estimates,MosaicsFit-method"
      ]
    },
    {
      "page": "export",
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      "topics": [
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        "export,MosaicsPeak-method"
      ]
    },
    {
      "page": "extractReads",
      "title": "Load read-level data and extract reads corresponding to each peak region",
      "topics": [
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        "extractReads,MosaicsPeak-method"
      ]
    },
    {
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        "filterPeak,MosaicsPeak-method"
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        "findSummit,MosaicsPeak-method"
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    {
      "page": "mosaicsFit",
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        "mosaicsFit,BinData-method"
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        "seqDepth,MosaicsFit-method",
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        "Getting started",
        "Identification of Punctuated Peaks using MOSAiCS",
        "Identification of Broad Peaks using MOSAiCS-HMM",
        "Post-processing Steps after Peak Calling",
        "Two-Sample Analysis using 'mosaicsRunAll'",
        "Two-Sample Analysis with Mappability and GC Content",
        "One-Sample Analysis",
        "Case Studies: Tuning Parameters to Improve the MOSAiCS Fit",
        "Conclusion and Ongoing Work",
        "Appendix: Example Lines of Aligned Read Files for SET ChIP-Seq Data",
        "Appendix: Example Lines of Aligned Read Files for PET ChIP-Seq Data",
        "Appendix: Chromosome Information File"
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