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  "Title": "Longitudinal system suitability monitoring and quality control\nfor proteomic experiments",
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  "Description": "MSstatsQC is an R package which provides longitudinal\nsystem suitability monitoring and quality control tools for\nproteomic experiments.",
  "License": "Artistic License 2.0",
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  "Date/Publication": "2026-04-28 12:46:29 UTC",
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        "DataProcess"
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      "source": "MSstatsQC.Rmd",
      "filename": "MSstatsQC.html",
      "title": "Longitudinal System Suitability Monitoring and Quality Control with MSstatsQC",
      "author": "Eralp Dogu eralp.dogu@gmail.com, Sara Taheri srtaheri66@gmail.com, Olga Vitek o.vitek@neu.edu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to MSstatsQC",
        "Key Features & Innovations",
        "Installation",
        "Input",
        "Example",
        "MSnbaseToMSstatsQC functions",
        "Arguments",
        "Data processing",
        "MSstatsQC core functions: control charts",
        "MSstatsQC core functions: XmRChart()",
        "MSstatsQC core functions: CUSUMChart()",
        "MSstatsQC core functions: ChangePointEstimator()",
        "MSstatsQC summary functions: river and radar plots",
        "MSstatsQC summary functions: decision map",
        "Use case: longitudinal profiling of DDA with missing values",
        "Use case: longitudinal profiling of QC with iRT peptides",
        "Use case: longitudinal profiling of QC from an SRM experiment",
        "MSstatsQC-ML functions: MSstatsQC-ML.trainR() and MSstatsQC.deployR()",
        "Output",
        "Project website",
        "Question and issues",
        "Citation",
        "Session information"
      ],
      "created": "2017-06-20 12:04:55",
      "modified": "2026-02-07 16:18:57",
      "commits": 32
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