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        "data.table",
        "data.frame"
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      "fields": [
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        "Reporter.intensity.count.0.M4R2",
        "Reporter.intensity.count.1.M4R2",
        "Reporter.intensity.count.2.M4R2",
        "Reporter.intensity.count.3.M4R2",
        "Reporter.intensity.count.4.M4R2",
        "Reporter.intensity.count.5.M4R2",
        "Reporter.intensity.count.6.M4R2",
        "Reporter.intensity.count.7.M4R2",
        "Reporter.intensity.count.8.M4R2",
        "Reporter.intensity.count.9.M4R2",
        "Reporter.intensity.count.0.M4R3",
        "Reporter.intensity.count.1.M4R3",
        "Reporter.intensity.count.2.M4R3",
        "Reporter.intensity.count.3.M4R3",
        "Reporter.intensity.count.4.M4R3",
        "Reporter.intensity.count.5.M4R3",
        "Reporter.intensity.count.6.M4R3",
        "Reporter.intensity.count.7.M4R3",
        "Reporter.intensity.count.8.M4R3",
        "Reporter.intensity.count.9.M4R3",
        "Reporter.intensity.count.0.M5R1",
        "Reporter.intensity.count.1.M5R1",
        "Reporter.intensity.count.2.M5R1",
        "Reporter.intensity.count.3.M5R1",
        "Reporter.intensity.count.4.M5R1",
        "Reporter.intensity.count.5.M5R1",
        "Reporter.intensity.count.6.M5R1",
        "Reporter.intensity.count.7.M5R1",
        "Reporter.intensity.count.8.M5R1",
        "Reporter.intensity.count.9.M5R1",
        "Reporter.intensity.count.0.M5R2",
        "Reporter.intensity.count.1.M5R2",
        "Reporter.intensity.count.2.M5R2",
        "Reporter.intensity.count.3.M5R2",
        "Reporter.intensity.count.4.M5R2",
        "Reporter.intensity.count.5.M5R2",
        "Reporter.intensity.count.6.M5R2",
        "Reporter.intensity.count.7.M5R2",
        "Reporter.intensity.count.8.M5R2",
        "Reporter.intensity.count.9.M5R2",
        "Reporter.intensity.count.0.M5R3",
        "Reporter.intensity.count.1.M5R3",
        "Reporter.intensity.count.2.M5R3",
        "Reporter.intensity.count.3.M5R3",
        "Reporter.intensity.count.4.M5R3",
        "Reporter.intensity.count.5.M5R3",
        "Reporter.intensity.count.6.M5R3",
        "Reporter.intensity.count.7.M5R3",
        "Reporter.intensity.count.8.M5R3",
        "Reporter.intensity.count.9.M5R3",
        "Sequence.coverage.M1R1....",
        "Sequence.coverage.M1R2....",
        "Sequence.coverage.M1R3....",
        "Sequence.coverage.M2R1....",
        "Sequence.coverage.M2R2....",
        "Sequence.coverage.M2R3....",
        "Sequence.coverage.M3R1....",
        "Sequence.coverage.M3R2....",
        "Sequence.coverage.M3R3....",
        "Sequence.coverage.M4R1....",
        "Sequence.coverage.M4R2....",
        "Sequence.coverage.M4R3....",
        "Sequence.coverage.M5R1....",
        "Sequence.coverage.M5R2....",
        "Sequence.coverage.M5R3....",
        "Intensity",
        "Intensity.M1R1",
        "Intensity.M1R2",
        "Intensity.M1R3",
        "Intensity.M2R1",
        "Intensity.M2R2",
        "Intensity.M2R3",
        "Intensity.M3R1",
        "Intensity.M3R2",
        "Intensity.M3R3",
        "Intensity.M4R1",
        "Intensity.M4R2",
        "Intensity.M4R3",
        "Intensity.M5R1",
        "Intensity.M5R2",
        "Intensity.M5R3",
        "iBAQ",
        "iBAQ.M1R1",
        "iBAQ.M1R2",
        "iBAQ.M1R3",
        "iBAQ.M2R1",
        "iBAQ.M2R2",
        "iBAQ.M2R3",
        "iBAQ.M3R1",
        "iBAQ.M3R2",
        "iBAQ.M3R3",
        "iBAQ.M4R1",
        "iBAQ.M4R2",
        "iBAQ.M4R3",
        "iBAQ.M5R1",
        "iBAQ.M5R2",
        "iBAQ.M5R3",
        "MS.MS.Count",
        "Only.identified.by.site",
        "Reverse",
        "Potential.contaminant",
        "id",
        "Peptide.IDs",
        "Peptide.is.razor",
        "Mod..peptide.IDs",
        "Evidence.IDs",
        "MS.MS.IDs",
        "Best.MS.MS",
        "Arg10.site.IDs",
        "Lys8.site.IDs",
        "Lys8.TMT6.site.IDs",
        "Oxidation..M..site.IDs",
        "Arg10.site.positions",
        "Lys8.site.positions",
        "Lys8.TMT6.site.positions",
        "Oxidation..M..site.positions"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "raw.mine",
      "title": "Example output file Spectromine",
      "object": "raw.mine",
      "file": "raw.mine.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "R.MS3.Used",
        "R.BlockName",
        "R.QuantificationMethod",
        "R.FileName",
        "PG.Genes",
        "PG.Organisms",
        "PG.ProteinAccessions",
        "PG.ProteinDescriptions",
        "PG.ProteinNames",
        "PG.UniprotIds",
        "PG.Coverage",
        "PG.QValue",
        "PEP.IsProteinGroupSpecific",
        "PEP.IsProteotypic",
        "PEP.StrippedSequence",
        "PEP.QValue",
        "PEP.IsUsedForQuantification",
        "PP.Charge",
        "P.MoleculeID",
        "PSM.TMT6_126..Raw.",
        "PSM.TMT6_127..Raw.",
        "PSM.TMT6_128..Raw.",
        "PSM.TMT6_129..Raw.",
        "PSM.TMT6_130..Raw.",
        "PSM.TMT6_131..Raw.",
        "PSM.IsUsedForQuantification",
        "PSM.NrOfMatchedChannelIons",
        "PSM.Qvalue"
      ],
      "rows": 170,
      "table": true,
      "tojson": true
    },
    {
      "name": "raw.om",
      "title": "Example output file Spectromine",
      "object": "raw.om",
      "file": "raw.om.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "RetentionTime",
        "ProteinName",
        "PeptideSequence",
        "Charge",
        "Channel",
        "Condition",
        "BioReplicate",
        "Run",
        "Mixture",
        "TechRepMixture",
        "Fraction",
        "Intensity",
        "Reference"
      ],
      "rows": 860,
      "table": true,
      "tojson": true
    },
    {
      "name": "raw.pd",
      "title": "Example output file PD",
      "object": "raw.pd",
      "file": "raw.pd.rda",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Checked",
        "Confidence",
        "Identifying.Node",
        "PSM.Ambiguity",
        "Annotated.Sequence",
        "Modifications",
        "Marked.as",
        "X..Protein.Groups",
        "X..Proteins",
        "Master.Protein.Accessions",
        "Master.Protein.Descriptions",
        "Protein.Accessions",
        "Protein.Descriptions",
        "X..Missed.Cleavages",
        "Charge",
        "DeltaScore",
        "DeltaCn",
        "Rank",
        "Search.Engine.Rank",
        "m.z..Da.",
        "MH...Da.",
        "Theo..MH...Da.",
        "DeltaM..ppm.",
        "Deltam.z..Da.",
        "Activation.Type",
        "MS.Order",
        "Isolation.Interference....",
        "Average.Reporter.S.N",
        "Ion.Inject.Time..ms.",
        "RT..min.",
        "First.Scan",
        "Spectrum.File",
        "File.ID",
        "Abundance..126",
        "Abundance..127N",
        "Abundance..127C",
        "Abundance..128N",
        "Abundance..128C",
        "Abundance..129N",
        "Abundance..129C",
        "Abundance..130N",
        "Abundance..130C",
        "Abundance..131",
        "Quan.Info",
        "Ions.Score",
        "Identity.Strict",
        "Identity.Relaxed",
        "Expectation.Value",
        "Percolator.q.Value",
        "Percolator.PEP"
      ],
      "rows": 2858,
      "table": true,
      "tojson": true
    },
    {
      "name": "tmt_pd_model",
      "title": "Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.",
      "object": "tmt_pd_model",
      "file": "tmt_pd_model.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tmt_pd_summarized",
      "title": "Example of TMT dataset processed using MSstatsTMT summarization function.",
      "object": "tmt_pd_summarized",
      "file": "tmt_pd_summarized.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "annotation.mine",
      "title": "Example annotation file for Spectromine",
      "topics": [
        "annotation.mine"
      ]
    },
    {
      "page": "annotation.mq",
      "title": "Example annotation file for MaxQuant",
      "topics": [
        "annotation.mq"
      ]
    },
    {
      "page": "annotation.pd",
      "title": "Example annotation file for PD",
      "topics": [
        "annotation.pd"
      ]
    },
    {
      "page": "apply_adj",
      "title": "Main PTM adjustment function",
      "topics": [
        "apply_adj"
      ]
    },
    {
      "page": "dia_skyline_model",
      "title": "Example of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.",
      "topics": [
        "dia_skyline_model"
      ]
    },
    {
      "page": "dia_skyline_summarized",
      "title": "Example of Sklyine DDA dataset processed using MSstats summarization function.",
      "topics": [
        "dia_skyline_summarized"
      ]
    },
    {
      "page": "evidence",
      "title": "Example evidence file for MaxQuant",
      "topics": [
        "evidence"
      ]
    },
    {
      "page": "example_dia_skyline",
      "title": "Example of input Sklyine DDA dataset.",
      "topics": [
        "example_dia_skyline"
      ]
    },
    {
      "page": "example_skyline_annotation",
      "title": "Example annotation file",
      "topics": [
        "example_skyline_annotation"
      ]
    },
    {
      "page": "expdesServer",
      "title": "Expdes Server module for future experiments",
      "topics": [
        "expdesServer"
      ]
    },
    {
      "page": "expdesUI",
      "title": "Expdes UI module for future experiments UI.",
      "topics": [
        "expdesUI"
      ]
    },
    {
      "page": "get_download_plot_filename",
      "title": "Get filename for plot download based on plot type",
      "topics": [
        "get_download_plot_filename"
      ]
    },
    {
      "page": "groupComparisonPlots2",
      "title": "Plotting funcitonality for QC plots",
      "topics": [
        "groupComparisonPlots2"
      ]
    },
    {
      "page": "helpUI",
      "title": "Help UI module for help page.",
      "topics": [
        "helpUI"
      ]
    },
    {
      "page": "homeUI",
      "title": "Home UI module for home page.",
      "topics": [
        "homeUI"
      ]
    },
    {
      "page": "launch_MSstatsShiny",
      "title": "Run MSstatsShiny Application",
      "topics": [
        "launch_MSstatsShiny"
      ]
    },
    {
      "page": "lf_model",
      "title": "Main LF modeling function for MSstatsShiny application",
      "topics": [
        "lf_model"
      ]
    },
    {
      "page": "lf_summarization_loop",
      "title": "Main LF calculation summarization function for MSstatsShiny application",
      "topics": [
        "lf_summarization_loop"
      ]
    },
    {
      "page": "loadpageServer",
      "title": "Loadpage Server module for data selection and upload server.",
      "topics": [
        "loadpageServer"
      ]
    },
    {
      "page": "loadpageUI",
      "title": "Loadpage UI module for data selection and upload UI.",
      "topics": [
        "loadpageUI"
      ]
    },
    {
      "page": "msstatsHelpUI",
      "title": "Help MSStats UI module for msstats help page.",
      "topics": [
        "msstatsHelpUI"
      ]
    },
    {
      "page": "msstatsTmtHelpUI",
      "title": "Help MSStats UI module for msstatstmt help page.",
      "topics": [
        "msstatsTmtHelpUI"
      ]
    },
    {
      "page": "networkUI",
      "title": "Network UI module for visualizing protein regulatory networks from INDRA.",
      "topics": [
        "networkUI"
      ]
    },
    {
      "page": "proteinGroups",
      "title": "Example ProteinGroups file for MaxQuant",
      "topics": [
        "proteinGroups"
      ]
    },
    {
      "page": "QC_check",
      "title": "Quick QC value check",
      "topics": [
        "QC_check"
      ]
    },
    {
      "page": "qcServer",
      "title": "QC Server module for data processing",
      "topics": [
        "qcServer"
      ]
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    {
      "page": "qcUI",
      "title": "QC UI module for data processing UI.",
      "topics": [
        "qcUI"
      ]
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    {
      "page": "radioTooltip",
      "title": "Custom function to create radio tool tips",
      "topics": [
        "radioTooltip"
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    {
      "page": "raw.mine",
      "title": "Example output file Spectromine",
      "topics": [
        "raw.mine"
      ]
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    {
      "page": "raw.om",
      "title": "Example output file Spectromine",
      "topics": [
        "raw.om"
      ]
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    {
      "page": "raw.pd",
      "title": "Example output file PD",
      "topics": [
        "raw.pd"
      ]
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    {
      "page": "server",
      "title": "Server function for the MSstatsShiny app",
      "topics": [
        "server"
      ]
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    {
      "page": "statmodelServer",
      "title": "Statmodel Server module for stat inference",
      "topics": [
        "statmodelServer"
      ]
    },
    {
      "page": "statmodelUI",
      "title": "Statmodel UI module for statistical inference UI.",
      "topics": [
        "statmodelUI"
      ]
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    {
      "page": "tmt_model",
      "title": "Main TMT modeling function for MSstatsShiny application",
      "topics": [
        "tmt_model"
      ]
    },
    {
      "page": "tmt_pd_model",
      "title": "Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.",
      "topics": [
        "tmt_pd_model"
      ]
    },
    {
      "page": "tmt_pd_summarized",
      "title": "Example of TMT dataset processed using MSstatsTMT summarization function.",
      "topics": [
        "tmt_pd_summarized"
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    {
      "page": "tmt_summarization_loop",
      "title": "Main TMT summarization calculation function for MSstatsShiny application",
      "topics": [
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    {
      "page": "uiObject",
      "title": "UI function for the MSstatsShiny app",
      "topics": [
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    {
      "page": "visualizeNetworkServer",
      "title": "Server logic for network visualization module",
      "topics": [
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    {
      "page": "xy_str",
      "title": "Simple function to return coordinates",
      "topics": [
        "xy_str"
      ]
    },
    {
      "page": "zip_and_copy_plot",
      "title": "Zip PDF files and copy to download destination",
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  "_rundeps": [
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