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  "Title": "Import Data from Various Mass Spectrometry Signal Processing\nTools to MSstats Format",
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  "Authors@R": "c(\nperson(\"Mateusz\", \"Staniak\", email = \"mtst@mstaniak.pl\", role = \"aut\"),\nperson(\"Devon\", \"Kohler\", email = \"kohler.d@northeastern.edu\", role = \"aut\"),\nperson(\"Anthony\", \"Wu\", email = \"wu.anthon@northeastern.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Meena\", \"Choi\", email = \"mnchoi67@gmail.com\", role = \"aut\"),\nperson(\"Ting\", \"Huang\", email = \"thuang0703@gmail.com\", role = \"aut\"),\nperson(\"Olga\", \"Vitek\", , email = \"o.vitek@northeastern.edu\", role = \"aut\"))",
  "Description": "MSstatsConvert provides tools for importing reports of\nMass Spectrometry data processing tools into R format suitable\nfor statistical analysis using the MSstats and MSstatsTMT\npackages.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "MassSpectrometry, Proteomics, Software, DataImport,\nQualityControl",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-02 22:29:16 UTC",
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  "Author": "Mateusz Staniak [aut],\nDevon Kohler [aut],\nAnthony Wu [aut, cre],\nMeena Choi [aut],\nTing Huang [aut],\nOlga Vitek [aut]",
  "Maintainer": "Anthony Wu <wu.anthon@northeastern.edu>",
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    {
      "page": "dot-cleanRawPD",
      "title": "Clean raw Proteome Discoverer data",
      "topics": [
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      "title": "Convert output of converters to data.frame",
      "topics": [
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    {
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      "title": "Convert output of converters to data.table",
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      "title": "Takes as input the output of the SpectronauttoMSstatsFormat function and calculates various quality metrics to assess the health of the data. Requires Anomaly Detection model to be fit.",
      "topics": [
        "CheckDataHealth"
      ]
    },
    {
      "page": "DIANNtoMSstatsFormat",
      "title": "Import Diann files",
      "topics": [
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    {
      "page": "DIAUmpiretoMSstatsFormat",
      "title": "Import DIA-Umpire files",
      "topics": [
        "DIAUmpiretoMSstatsFormat"
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    {
      "page": "FragPipetoMSstatsFormat",
      "title": "Import FragPipe files",
      "topics": [
        "FragPipetoMSstatsFormat"
      ]
    },
    {
      "page": "getInputFile",
      "title": "Get one of files contained in an instance of 'MSstatsInputFiles' class.",
      "topics": [
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        "getInputFile,MSstatsInputFiles-method",
        "getInputFile,MSstatsPhilosopherFiles-method"
      ]
    },
    {
      "page": "MaxQtoMSstatsFormat",
      "title": "Import MaxQuant files",
      "topics": [
        "MaxQtoMSstatsFormat"
      ]
    },
    {
      "page": "MaxQtoMSstatsTMTFormat",
      "title": "Generate MSstatsTMT required input format from MaxQuant output",
      "topics": [
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    {
      "page": "MetamorpheusToMSstatsFormat",
      "title": "Import Metamorpheus files",
      "topics": [
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      ]
    },
    {
      "page": "MSstatsAnomalyScores",
      "title": "Run Anomaly Model",
      "topics": [
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    {
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      "title": "Creates balanced design by removing overlapping fractions and filling incomplete rows",
      "topics": [
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    {
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      "topics": [
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        "MSstatsClean,MSstatsDIANNFiles-method",
        "MSstatsClean,MSstatsDIAUmpireFiles-method",
        "MSstatsClean,MSstatsMaxQuantFiles-method",
        "MSstatsClean,MSstatsMetamorpheusFiles-method",
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        "MSstatsClean,MSstatsPhilosopherFiles-method",
        "MSstatsClean,MSstatsProgenesisFiles-method",
        "MSstatsClean,MSstatsProteinProspectorFiles-method",
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    {
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      "topics": [
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      "topics": [
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      "title": "Import OpenSWATH files",
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