{
  "_id": "6a1a74931d7bb097a09d1871",
  "Package": "MSstats",
  "Title": "Protein Significance Analysis in DDA, SRM and DIA for Label-free\nor Label-based Proteomics Experiments",
  "Version": "4.21.0",
  "Date": "2025-03-05",
  "Description": "A set of tools for statistical relative protein\nsignificance analysis in DDA, SRM and DIA experiments.",
  "Authors@R": "c(\nperson(\"Meena\", \"Choi\", email = \"mnchoi67@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Mateusz\", \"Staniak\", email = \"mtst@mstaniak.pl\", role = \"aut\"),\nperson(\"Devon\", \"Kohler\", email = \"kohler.d@northeastern.edu\", role = \"aut\"),\nperson(\"Tony\", \"Wu\", email = \"wu.anthon@northeastern.edu\", role = \"aut\"),\nperson(\"Deril\", \"Raju\", email = \"raju.d@northeastern.edu\", role = \"aut\"),\nperson(\"Tsung-Heng\", \"Tsai\", email = \"tsai.tsungheng@gmail.com\", role = \"aut\"),\nperson(\"Ting\", \"Huang\", email = \"thuang0703@gmail.com\", role = \"aut\"),\nperson(\"Olga\", \"Vitek\", email = \"o.vitek@northeastern.edu\", role = \"aut\"))",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, MassSpectrometry, Proteomics, Software,\nNormalization, QualityControl, TimeCourse",
  "LazyData": "true",
  "URL": "http://msstats.org",
  "BugReports": "https://groups.google.com/forum/#!forum/msstats",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-28 14:50:01 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:18 UTC",
  "RemoteUrl": "https://github.com/bioc/MSstats",
  "RemoteRef": "HEAD",
  "RemoteSha": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
  "Author": "Meena Choi [aut, cre],\nMateusz Staniak [aut],\nDevon Kohler [aut],\nTony Wu [aut],\nDeril Raju [aut],\nTsung-Heng Tsai [aut],\nTing Huang [aut],\nOlga Vitek [aut]",
  "Maintainer": "Meena Choi <mnchoi67@gmail.com>",
  "MD5sum": "7ed0a7725660f03c62aa5cdb262df4c7",
  "_user": "bioc",
  "_type": "src",
  "_file": "MSstats_4.21.0.tar.gz",
  "_fileid": "57bf07c73d0439d2e209db5a37764269693a567b2417d94e761cbc4838a82b67",
  "_filesize": 2183617,
  "_sha256": "57bf07c73d0439d2e209db5a37764269693a567b2417d94e761cbc4838a82b67",
  "_created": "2026-05-28T14:50:01.000Z",
  "_published": "2026-05-30T05:24:35.265Z",
  "_jobs": [
    {
      "job": 78626276585,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7305635208"
    },
    {
      "job": 78626276870,
      "time": 253,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7269217426"
    },
    {
      "job": 78626276799,
      "time": 282,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7269259475"
    },
    {
      "job": 78626276841,
      "time": 248,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7269216250"
    },
    {
      "job": 78626276857,
      "time": 354,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7269285943"
    },
    {
      "job": 78626276647,
      "time": 74,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78626276648,
      "time": 179,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78626276846,
      "time": 139,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7270322639"
    },
    {
      "job": 78626276805,
      "time": 472,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7270341531"
    },
    {
      "job": 78626276596,
      "time": 338,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269107195"
    },
    {
      "job": 78626276791,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269205294"
    },
    {
      "job": 78626276777,
      "time": 224,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7269226594"
    },
    {
      "job": 78626276641,
      "time": 73,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78626276886,
      "time": 240,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7269233069"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 21
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MSstats",
  "_commit": {
    "id": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379898
  },
  "_maintainer": {
    "name": "Meena Choi",
    "email": "mnchoi67@gmail.com",
    "login": "meenachoi",
    "description": "",
    "uuid": 4159931
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "MSstatsConvert",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "htmltools",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "marray",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "statmod",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "mockery",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-27",
      "n": 4
    },
    {
      "week": "2025-35",
      "n": 2
    },
    {
      "week": "2025-37",
      "n": 2
    },
    {
      "week": "2025-38",
      "n": 2
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-42",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 3
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 4
    },
    {
      "week": "2026-15",
      "n": 4
    },
    {
      "week": "2026-16",
      "n": 9
    },
    {
      "week": "2026-17",
      "n": 7
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "4.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "4.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "massspectrometry",
    "proteomics",
    "software",
    "normalization",
    "qualitycontrol",
    "timecourse",
    "openblas",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1335,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MSstats"
  },
  "_mentions": 115,
  "_searchresults": 383,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MSstats.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkRepeatedDesign",
    "dataProcess",
    "dataProcessPlots",
    "designSampleSize",
    "designSampleSizePlots",
    "DIANNtoMSstatsFormat",
    "DIAUmpiretoMSstatsFormat",
    "extractSDRF",
    "FragPipetoMSstatsFormat",
    "getProcessed",
    "getSamplesInfo",
    "getSelectedProteins",
    "groupComparison",
    "groupComparisonPlots",
    "groupComparisonQCPlots",
    "makePeptidesDictionary",
    "MaxQtoMSstatsFormat",
    "modelBasedQCPlots",
    "MSstatsContrastMatrix",
    "MSstatsGroupComparison",
    "MSstatsGroupComparisonOutput",
    "MSstatsGroupComparisonSingleProtein",
    "MSstatsHandleMissing",
    "MSstatsMergeFractions",
    "MSstatsNormalize",
    "MSstatsPrepareForDataProcess",
    "MSstatsPrepareForGroupComparison",
    "MSstatsPrepareForSummarization",
    "MSstatsQualityMetricsPlot",
    "MSstatsSelectFeatures",
    "MSstatsSummarizationOutput",
    "MSstatsSummarizeSingleLinear",
    "MSstatsSummarizeSingleTMP",
    "MSstatsSummarizeWithSingleCore",
    "OpenMStoMSstatsFormat",
    "OpenSWATHtoMSstatsFormat",
    "PDtoMSstatsFormat",
    "ProgenesistoMSstatsFormat",
    "quantification",
    "savePlot",
    "SDRFtoAnnotation",
    "SkylinetoMSstatsFormat",
    "SpectronauttoMSstatsFormat",
    "theme_msstats",
    "validateAnnotation"
  ],
  "_datasets": [
    {
      "name": "DDARawData",
      "title": "Example dataset from a label-free DDA, a controlled spike-in experiment.",
      "object": "DDARawData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "PeptideSequence",
        "PrecursorCharge",
        "FragmentIon",
        "ProductCharge",
        "IsotopeLabelType",
        "Condition",
        "BioReplicate",
        "Run",
        "Intensity"
      ],
      "rows": 2070,
      "table": true,
      "tojson": true
    },
    {
      "name": "DDARawData.Skyline",
      "title": "Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.",
      "object": "DDARawData.Skyline",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "PeptideSequence",
        "PrecursorCharge",
        "FragmentIon",
        "ProductCharge",
        "IsotopeLabelType",
        "Condition",
        "BioReplicate",
        "FileName",
        "Area",
        "StandardType",
        "Truncated"
      ],
      "rows": 11934,
      "table": true,
      "tojson": true
    },
    {
      "name": "DIARawData",
      "title": "Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.",
      "object": "DIARawData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "PeptideSequence",
        "PrecursorCharge",
        "FragmentIon",
        "ProductCharge",
        "IsotopeLabelType",
        "Condition",
        "BioReplicate",
        "Run",
        "Intensity"
      ],
      "rows": 980,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_SDRF",
      "title": "Example SDRF.",
      "object": "example_SDRF",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "source.name",
        "characteristics.organism.",
        "characteristics.organism.part.",
        "characteristics.age.",
        "characteristics.developmental.stage.",
        "characteristics.sex.",
        "characteristics.ancestry.category.",
        "characteristics.disease.",
        "characteristics.cell.type.",
        "characteristics.individual.",
        "characteristics.biological.replicate.",
        "material.type",
        "assay.name",
        "technology.type",
        "comment.fractionation.method.",
        "comment.technical.replicate.",
        "comment.fraction.identifier.",
        "comment.file.uri.",
        "comment.ms2.mass.analyzer.",
        "comment.instrument.",
        "comment.separation.",
        "comment.label.",
        "comment.cleavage.agent.details.",
        "comment.modification.parameters.",
        "comment.modification.parameters..1",
        "comment.precursor.mass.tolerance.",
        "comment.fragment.mass.tolerance.",
        "comment.data.file."
      ],
      "rows": 160,
      "table": true,
      "tojson": true
    },
    {
      "name": "SRMRawData",
      "title": "Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study",
      "object": "SRMRawData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "PeptideSequence",
        "PrecursorCharge",
        "FragmentIon",
        "ProductCharge",
        "IsotopeLabelType",
        "Condition",
        "BioReplicate",
        "Run",
        "Intensity"
      ],
      "rows": 720,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "checkRepeatedDesign",
      "title": "Check if data represents repeated measurements design",
      "topics": [
        "checkRepeatedDesign"
      ]
    },
    {
      "page": "dataProcess",
      "title": "Process MS data: clean, normalize and summarize before differential analysis",
      "topics": [
        "dataProcess"
      ]
    },
    {
      "page": "dataProcessPlots",
      "title": "Visualization for explanatory data analysis",
      "topics": [
        "dataProcessPlots"
      ]
    },
    {
      "page": "DDARawData",
      "title": "Example dataset from a label-free DDA, a controlled spike-in experiment.",
      "topics": [
        "DDARawData"
      ]
    },
    {
      "page": "DDARawData.Skyline",
      "title": "Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.",
      "topics": [
        "DDARawData.Skyline"
      ]
    },
    {
      "page": "designSampleSize",
      "title": "Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation",
      "topics": [
        "designSampleSize"
      ]
    },
    {
      "page": "designSampleSizePlots",
      "title": "Visualization for sample size calculation",
      "topics": [
        "designSampleSizePlots"
      ]
    },
    {
      "page": "DIARawData",
      "title": "Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.",
      "topics": [
        "DIARawData"
      ]
    },
    {
      "page": "example_SDRF",
      "title": "Example SDRF.",
      "topics": [
        "example_SDRF"
      ]
    },
    {
      "page": "extractSDRF",
      "title": "Extract experimental design from MSstats format into SDRF format",
      "topics": [
        "extractSDRF"
      ]
    },
    {
      "page": "getProcessed",
      "title": "Get feature-level data to be used in the MSstatsSummarizationOutput function",
      "topics": [
        "getProcessed"
      ]
    },
    {
      "page": "getSamplesInfo",
      "title": "Get information about number of measurements for each group",
      "topics": [
        "getSamplesInfo"
      ]
    },
    {
      "page": "getSelectedProteins",
      "title": "Get proteins based on names or integer IDs",
      "topics": [
        "getSelectedProteins"
      ]
    },
    {
      "page": "groupComparison",
      "title": "Whole plot testing",
      "topics": [
        "groupComparison"
      ]
    },
    {
      "page": "groupComparisonPlots",
      "title": "Visualization for model-based analysis and summarizing differentially abundant proteins",
      "topics": [
        "groupComparisonPlots"
      ]
    },
    {
      "page": "groupComparisonQCPlots",
      "title": "Visualization for model-based quality control in fitting model",
      "topics": [
        "groupComparisonQCPlots"
      ]
    },
    {
      "page": "makePeptidesDictionary",
      "title": "Prepare a peptides dictionary for global standards normalization",
      "topics": [
        "makePeptidesDictionary"
      ]
    },
    {
      "page": "modelBasedQCPlots",
      "title": "Visualization for model-based quality control in fitting model",
      "topics": [
        "modelBasedQCPlots"
      ]
    },
    {
      "page": "MSstatsContrastMatrix",
      "title": "Create a contrast matrix for groupComparison function",
      "topics": [
        "MSstatsContrastMatrix"
      ]
    },
    {
      "page": "MSstatsGroupComparison",
      "title": "Group comparison",
      "topics": [
        "MSstatsGroupComparison"
      ]
    },
    {
      "page": "MSstatsGroupComparisonOutput",
      "title": "Create output of group comparison based on results for individual proteins",
      "topics": [
        "MSstatsGroupComparisonOutput"
      ]
    },
    {
      "page": "MSstatsGroupComparisonSingleProtein",
      "title": "Group comparison for a single protein",
      "topics": [
        "MSstatsGroupComparisonSingleProtein"
      ]
    },
    {
      "page": "MSstatsHandleMissing",
      "title": "Handle censored missing values",
      "topics": [
        "MSstatsHandleMissing"
      ]
    },
    {
      "page": "MSstatsMergeFractions",
      "title": "Re-format the data before feature selection",
      "topics": [
        "MSstatsMergeFractions"
      ]
    },
    {
      "page": "MSstatsNormalize",
      "title": "Normalize MS data",
      "topics": [
        "MSstatsNormalize"
      ]
    },
    {
      "page": "MSstatsPrepareForDataProcess",
      "title": "Prepare data for processing by `dataProcess` function",
      "topics": [
        "MSstatsPrepareForDataProcess"
      ]
    },
    {
      "page": "MSstatsPrepareForGroupComparison",
      "title": "Prepare output for dataProcess for group comparison",
      "topics": [
        "MSstatsPrepareForGroupComparison"
      ]
    },
    {
      "page": "MSstatsPrepareForSummarization",
      "title": "Prepare feature-level data for protein-level summarization",
      "topics": [
        "MSstatsPrepareForSummarization"
      ]
    },
    {
      "page": "MSstatsQualityMetricsPlot",
      "title": "Plot quality metrics from converter output",
      "topics": [
        "MSstatsQualityMetricsPlot"
      ]
    },
    {
      "page": "MSstatsSelectFeatures",
      "title": "Feature selection before feature-level data summarization",
      "topics": [
        "MSstatsSelectFeatures"
      ]
    },
    {
      "page": "MSstatsSummarizationOutput",
      "title": "Post-processing output from MSstats summarization",
      "topics": [
        "MSstatsSummarizationOutput"
      ]
    },
    {
      "page": "MSstatsSummarizeSingleLinear",
      "title": "Linear model-based summarization for a single protein",
      "topics": [
        "MSstatsSummarizeSingleLinear"
      ]
    },
    {
      "page": "MSstatsSummarizeSingleTMP",
      "title": "Tukey Median Polish summarization for a single protein",
      "topics": [
        "MSstatsSummarizeSingleTMP"
      ]
    },
    {
      "page": "MSstatsSummarizeWithMultipleCores",
      "title": "Feature-level data summarization with multiple cores",
      "topics": [
        "MSstatsSummarizeWithMultipleCores"
      ]
    },
    {
      "page": "MSstatsSummarizeWithSingleCore",
      "title": "Feature-level data summarization with 1 core",
      "topics": [
        "MSstatsSummarizeWithSingleCore"
      ]
    },
    {
      "page": "quantification",
      "title": "Protein sample quantification or group quantification",
      "topics": [
        "quantification"
      ]
    },
    {
      "page": "savePlot",
      "title": "Save a plot to pdf file",
      "topics": [
        "savePlot"
      ]
    },
    {
      "page": "SDRFtoAnnotation",
      "title": "Convert SDRF experimental design file into an MSstats annotation file",
      "topics": [
        "SDRFtoAnnotation"
      ]
    },
    {
      "page": "SRMRawData",
      "title": "Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study",
      "topics": [
        "SRMRawData"
      ]
    },
    {
      "page": "theme_msstats",
      "title": "Theme for MSstats plots",
      "topics": [
        "theme_msstats"
      ]
    },
    {
      "page": "validateAnnotation",
      "title": "Check if annotation matches intended experimental design",
      "topics": [
        "validateAnnotation"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MSstats/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "backports",
    "base64enc",
    "bitops",
    "boot",
    "bslib",
    "cachem",
    "caTools",
    "checkmate",
    "cli",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "ggrepel",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "lme4",
    "log4r",
    "magrittr",
    "marray",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "minqa",
    "MSstatsConvert",
    "nlme",
    "nloptr",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "preprocessCore",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "MSstatsWorkflow.Rmd",
      "filename": "MSstatsWorkflow.html",
      "title": "MSstats: End to End Workflow",
      "engine": "knitr::knitr",
      "headings": [
        "MSstats: Protein/Peptide significance analysis",
        "Introduction",
        "Installation",
        "1. Workflow",
        "1.1 Raw Data",
        "1.2 Loading PD Data to MSstats",
        "1.3 Converters",
        "1.4 Data Process",
        "1.4.1 Data Processing Options",
        "Normalization",
        "Feature Selection",
        "Missing Value Imputation",
        "1.4.2 Data Process Plots",
        "__1.5 Modeling __",
        "1.5.1 How to Account for Covariates",
        "Step 1: Set up your conditions",
        "Step 2: Create a contrast matrix",
        "1.5.2 groupComparisonPlot",
        "1.6 GroupComparisonQCPlots",
        "1.7 Sample Size Calculation",
        "1.7.1 Sample Size Calculation Plot",
        "1.8 Quantification from groupComparison Data"
      ],
      "created": "2024-10-15 21:28:14",
      "modified": "2025-03-12 21:32:27",
      "commits": 3
    },
    {
      "source": "MSstats.Rmd",
      "filename": "MSstats.html",
      "title": "MSstats: Protein/Peptide significance analysis",
      "engine": "knitr::knitr",
      "headings": [
        "MSstats: Protein/Peptide significance analysis",
        "SkylinetoMSstatsFormat",
        "Arguments",
        "Example",
        "MaxQtoMSstatsFormat",
        "ProgenesistoMSstatsFormat",
        "SpectronauttoMSstatsFormat",
        "dataProcess",
        "Details of outputs",
        "RunlevelData from dataProcess",
        "ComparisonResult from groupComparison : one or two columns will be added.",
        "dataProcessPlots",
        "groupComparison",
        "groupComparisonPlots",
        "modelBasedQCPlots",
        "designSampleSize",
        "designSampleSizePlots",
        "quantification"
      ],
      "created": "2015-10-01 18:42:29",
      "modified": "2023-07-28 13:33:12",
      "commits": 11
    },
    {
      "source": "MSstatsPlus.Rmd",
      "filename": "MSstatsPlus.html",
      "title": "MSstats+: Peak quality-weighted differential analysis",
      "engine": "knitr::knitr",
      "headings": [
        "MSstats+: Peak quality-weighted differential analysis",
        "Load packages",
        "Converter",
        "Load data",
        "Run converter",
        "Check model fit",
        "Manual formatting and data conversion",
        "Data processing and summarization",
        "Differential analysis",
        "Compare results to base MSstats",
        "MSstatsBig"
      ],
      "created": "2025-09-10 19:27:16",
      "modified": "2026-01-22 17:54:26",
      "commits": 2
    }
  ],
  "_score": 9.411110576114744,
  "_indexed": true,
  "_nocasepkg": "msstats",
  "_universes": [
    "bioc",
    "meenachoi"
  ],
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.19.2",
      "date": "2026-04-17T07:08:27.000Z",
      "arch": "aarch64",
      "commit": "1c9655510a77e6fe2ad3f89c8e248b7c8240b2ca",
      "fileid": "b13b00ae7829d02ae36ba8a64f522ae78009d4da5fb2864e6eac5707a772fbfd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24552230266"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.19.2",
      "date": "2026-04-17T07:10:39.000Z",
      "arch": "x86_64",
      "commit": "1c9655510a77e6fe2ad3f89c8e248b7c8240b2ca",
      "fileid": "b5e0b40f77feeae80c2de2179ab29a9083ebfaadc060e10b4c7f211ada4555f4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24552230266"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "4.19.2",
      "date": "2026-04-17T07:08:31.000Z",
      "arch": "x86_64",
      "commit": "1c9655510a77e6fe2ad3f89c8e248b7c8240b2ca",
      "fileid": "319b5f751cdf150f460047a536d13b20829f2d06cec77be661f9f1d357d7dd18",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24552230266"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.21.0",
      "date": "2026-05-28T14:53:28.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "b2bf30a58bb4bc2cb0d207c4525d4874c11ac50b64d4aa8454624eea461bc4c6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.21.0",
      "date": "2026-05-28T14:54:50.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "c233a1920f7887bf6e950da49d83bb762bfb2c6fe40eeeafec560862e20adb02",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "4.21.0",
      "date": "2026-05-28T14:53:18.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "5745bd95207343e20f2bdd55c01112d867b881a5d5e843f2ab38f945387743d6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "4.21.0",
      "date": "2026-05-28T14:55:56.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "1a3a961b5ed26ba14ab8eb4065be5ed3349bd1d7a7502437ad57a327c8224d87",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "4.21.0",
      "date": "2026-05-28T15:37:56.000Z",
      "arch": "aarch64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "35b7fbb5d326c0517b34eb597676fa655aad8cabf41904478b28240afef41787",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "4.21.0",
      "date": "2026-05-28T15:35:47.000Z",
      "arch": "x86_64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "0b84f7d9645e08bd689619ad3ac2546ad6cda53f21b7c97d67544c8bc07a46b4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.21.0",
      "date": "2026-05-28T14:54:18.000Z",
      "arch": "emscripten",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "5b2c7a2ae0b3df3e15d67c74dae02f2a8fce197b6a341ab0609f4734a2f2bb99",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.21.0",
      "date": "2026-05-28T14:52:51.000Z",
      "arch": "x86_64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "b367cd7266c6bbd357dd63533285c61c03d7eac1f35bfa9df07db5a7044edad1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "4.21.0",
      "date": "2026-05-28T14:53:05.000Z",
      "arch": "x86_64",
      "commit": "a186133bc90f7b4ffb734fccd395fd223f48b34f",
      "fileid": "e10536bf03c3e7071a6988ddbb75c4b0146f6cb5b2f8e6ae3ca01322ab5acfc6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581804727"
    }
  ]
}