{
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  "Package": "QFeatures",
  "Title": "Quantitative features for mass spectrometry data",
  "Version": "1.23.1",
  "Authors@R": "c(person(\"Laurent\", \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = c(\"aut\", \"cre\")),\nperson(\"Christophe\", \"Vanderaa\",\nemail = \"christophe.vanderaa@uclouvain.be\",\ncomment = c(ORCID = \"0000-0001-7443-5427\"),\nrole = \"aut\"),\nperson(\"Karolína\", \"Kryštofová\",\ncomment = c(ORCID = \"0009-0004-2896-2188\"),\nrole = \"ctb\"),\nperson(\"Léopold\", \"Guyot\",\nemail = \"leopold.guyot@uclouvain.be\",\nrole = \"ctb\"))",
  "Description": "The QFeatures infrastructure enables the management and\nprocessing of quantitative features for high-throughput mass\nspectrometry assays. It provides a familiar Bioconductor user\nexperience to manages quantitative data across different assay\nlevels (such as peptide spectrum matches, peptides and\nproteins) in a coherent and tractable format.",
  "biocViews": "Infrastructure, MassSpectrometry, Proteomics, Metabolomics",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/rformassspectrometry/QFeatures/issues",
  "URL": "https://rformassspectrometry.github.io/QFeatures",
  "Collate": "'AllGenerics.R' 'AssayLinks.R' 'QFeatures-class.R'\n'QFeatures-functions.R' 'QFeatures-longForm.R'\n'QFeatures-processing.R' 'QFeatures-filter.R'\n'QFeatures-missing-data.R' 'QFeatures-aggregation.R'\n'QFeatures-imputation.R' 'QFeatures-join.R'\n'QFeatures-validity.R' 'SummarizedExperiment-methods.R'\n'subsetBy-methods.R' 'readQFeatures.R'\n'readQFeaturesFromDIANN.R' 'data.R' 'reduce.R' 'utils.R'\n'display.R'",
  "Roxygen": "list(markdown=TRUE)",
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  "Repository": "https://rformassspectrometry.r-universe.dev",
  "Date/Publication": "2026-05-03 15:27:22 UTC",
  "RemoteUrl": "https://github.com/rformassspectrometry/qfeatures",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-23 11:11:22 UTC",
    "User": "root"
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  "Author": "Laurent Gatto [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1520-2268>),\nChristophe Vanderaa [aut] (ORCID:\n<https://orcid.org/0000-0001-7443-5427>),\nKarolína Kryštofová [ctb] (ORCID:\n<https://orcid.org/0009-0004-2896-2188>),\nLéopold Guyot [ctb]",
  "Maintainer": "Laurent Gatto <laurent.gatto@uclouvain.be>",
  "_user": "rformassspectrometry",
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  "_expires": "2026-10-31T11:39:39.000Z",
  "_created": "2026-07-23T11:11:22.000Z",
  "_published": "2026-07-23T11:39:41.374Z",
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  "_homeurl": "https://github.com/rformassspectrometry/qfeatures",
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  "_exports": [
    "addAssay",
    "addAssayLink",
    "addAssayLinkOneToOne",
    "adjacencyMatrix",
    "adjacencyMatrix<-",
    "aggcounts",
    "aggregateFeatures",
    "assayLink",
    "AssayLink",
    "assayLinks",
    "AssayLinks",
    "coerce",
    "countUniqueFeatures",
    "createPrecursorId",
    "dims",
    "display",
    "dropEmptyAssays",
    "expandDataFrame",
    "filterFeatures",
    "filterNA",
    "getQFeaturesType",
    "impute",
    "infIsNA",
    "isDuplicated",
    "joinAssays",
    "logTransform",
    "longForm",
    "longFormat",
    "ncols",
    "nNA",
    "normalize",
    "nrows",
    "QFeatures",
    "rbindRowData",
    "readQFeatures",
    "readQFeaturesFromDIANN",
    "readSummarizedExperiment",
    "reduceDataFrame",
    "removeAssay",
    "replaceAssay",
    "replaceColnames",
    "rowData<-",
    "rowDataNames",
    "scaleTransform",
    "selectRowData",
    "setQFeaturesType",
    "show",
    "subsetByFeature",
    "sweep",
    "unfoldDataFrame",
    "updateObject",
    "validQFeaturesTypes",
    "VariableFilter",
    "zeroIsNA"
  ],
  "_datasets": [
    {
      "name": "feat1",
      "title": "Feature example data",
      "object": "feat1",
      "file": "feat1.rda",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "feat2",
      "title": "Feature example data",
      "object": "feat2",
      "file": "feat2.rda",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "feat3",
      "title": "Example 'QFeatures' object after processing",
      "object": "feat3",
      "file": "feat3.rda",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "feat4",
      "title": "Example 'QFeatures'",
      "object": "feat4",
      "file": "feat4.rda",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ft_na",
      "title": "Feature example data",
      "object": "ft_na",
      "file": "ft_na.rda",
      "class": [
        "QFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hlpsms",
      "title": "hyperLOPIT PSM-level expression data",
      "object": "hlpsms",
      "file": "hlpsms.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X126",
        "X127C",
        "X127N",
        "X128C",
        "X128N",
        "X129C",
        "X129N",
        "X130C",
        "X130N",
        "X131",
        "Sequence",
        "ProteinDescriptions",
        "NbProteins",
        "ProteinGroupAccessions",
        "Modifications",
        "qValue",
        "PEP",
        "IonScore",
        "NbMissedCleavages",
        "IsolationInterference",
        "IonInjectTimems",
        "Intensity",
        "Charge",
        "mzDa",
        "MHDa",
        "DeltaMassPPM",
        "RTmin",
        "markers"
      ],
      "rows": 3010,
      "table": true,
      "tojson": true
    },
    {
      "name": "se_na2",
      "title": "Feature example data",
      "object": "se_na2",
      "file": "se_na2.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "QFeatures-aggregate",
      "title": "Aggregate assays' quantitative features",
      "topics": [
        "adjacencyMatrix,QFeatures-method",
        "adjacencyMatrix,SummarizedExperiment-method",
        "adjacencyMatrix<-",
        "aggcounts",
        "aggcounts,SummarizedExperiment-method",
        "aggregateFeatures",
        "aggregateFeatures,QFeatures-method",
        "aggregateFeatures,SummarizedExperiment-method"
      ]
    },
    {
      "page": "AllGenerics",
      "title": "Placeholder for generics functions documentation",
      "topics": [
        "AllGenerics"
      ]
    },
    {
      "page": "AssayLinks",
      "title": "Links between Assays",
      "topics": [
        "addAssayLink",
        "addAssayLinkOneToOne",
        "AssayLink",
        "assayLink",
        "AssayLink-class",
        "AssayLinks",
        "assayLinks",
        "AssayLinks-class",
        "class:AssayLink",
        "class:AssayLinks",
        "show,AssayLink-method",
        "updateObject,AssayLink-method",
        "updateObject,AssayLinks-method",
        "[,AssayLink,character,ANY,ANY-method",
        "[,AssayLink,character-method",
        "[,AssayLinks,character-method",
        "[,AssayLinks,list,ANY,ANY-method"
      ]
    },
    {
      "page": "countUniqueFeatures",
      "title": "Count Unique Features",
      "topics": [
        "countUniqueFeatures"
      ]
    },
    {
      "page": "createPrecursorId",
      "title": "Create precursor identfiers",
      "topics": [
        "createPrecursorId"
      ]
    },
    {
      "page": "display",
      "title": "Interactive MultiAssayExperiment Explorer",
      "topics": [
        "display"
      ]
    },
    {
      "page": "feat1",
      "title": "Feature example data",
      "topics": [
        "feat1",
        "feat2",
        "ft_na",
        "se_na2"
      ]
    },
    {
      "page": "feat3",
      "title": "Example 'QFeatures' object after processing",
      "topics": [
        "feat3"
      ]
    },
    {
      "page": "feat4",
      "title": "Example 'QFeatures'",
      "topics": [
        "feat4"
      ]
    },
    {
      "page": "hlpsms",
      "title": "hyperLOPIT PSM-level expression data",
      "topics": [
        "hlpsms"
      ]
    },
    {
      "page": "impute",
      "title": "Quantitative proteomics data imputation",
      "topics": [
        "impute",
        "impute,QFeatures-method",
        "impute,SummarizedExperiment-method"
      ]
    },
    {
      "page": "joinAssays",
      "title": "Join assays in a QFeatures object",
      "topics": [
        "joinAssays"
      ]
    },
    {
      "page": "QFeatures-longForm",
      "title": "Reshape into a long data format",
      "topics": [
        "longForm",
        "longForm,QFeatures",
        "longForm,QFeatures-method",
        "longForm,SummarizedExperiment",
        "longForm,SummarizedExperiment-method",
        "longFormat"
      ]
    },
    {
      "page": "QFeatures-missing-data",
      "title": "Managing missing data",
      "topics": [
        "filterNA",
        "filterNA,QFeatures-method",
        "filterNA,SummarizedExperiment-method",
        "infIsNA",
        "infIsNA,QFeatures,character-method",
        "infIsNA,QFeatures,integer-method",
        "infIsNA,QFeatures,missing-method",
        "infIsNA,QFeatures,numeric-method",
        "infIsNA,SummarizedExperiment,missing-method",
        "missing-data",
        "nNA",
        "nNA,QFeatures,character-method",
        "nNA,QFeatures,integer-method",
        "nNA,QFeatures,missing-method",
        "nNA,QFeatures,numeric-method",
        "nNA,SummarizedExperiment,missing-method",
        "zeroIsNA",
        "zeroIsNA,QFeatures,character-method",
        "zeroIsNA,QFeatures,integer-method",
        "zeroIsNA,QFeatures,missing-method",
        "zeroIsNA,QFeatures,numeric-method",
        "zeroIsNA,SummarizedExperiment,missing-method"
      ]
    },
    {
      "page": "QFeatures-class",
      "title": "Quantitative MS QFeatures",
      "topics": [
        "addAssay",
        "c,QFeatures-method",
        "class:QFeatures",
        "coerce,MultiAssayExperiment,QFeatures-method",
        "coerce-QFeatures",
        "dims,QFeatures-method",
        "dropEmptyAssays",
        "names<-,QFeatures,character-method",
        "ncols,QFeatures-method",
        "nrows,QFeatures-method",
        "plot.QFeatures",
        "QFeatures",
        "QFeatures-class",
        "rbindRowData",
        "removeAssay",
        "replaceAssay",
        "replaceColnames",
        "rowData,QFeatures-method",
        "rowData<-,QFeatures,ANY-method",
        "rowData<-,QFeatures,DataFrameList-method",
        "rowDataNames",
        "selectRowData",
        "show,QFeatures-method",
        "updateObject,QFeatures-method",
        "[,QFeatures,ANY,ANY,ANY-method",
        "[,QFeatures,character,ANY,ANY-method",
        "[[<-,QFeatures,ANY,ANY-method"
      ]
    },
    {
      "page": "QFeatures-filtering",
      "title": "Filter features based on their rowData",
      "topics": [
        "CharacterVariableFilter",
        "CharacterVariableFilter-class",
        "filterFeatures",
        "filterFeatures,QFeatures,AnnotationFilter-method",
        "filterFeatures,QFeatures,formula-method",
        "isDuplicated",
        "NumericVariableFilter",
        "NumericVariableFilter-class",
        "QFeatures-filtering",
        "VariableFilter"
      ]
    },
    {
      "page": "QFeatures-processing",
      "title": "QFeatures processing",
      "topics": [
        "logTransform",
        "logTransform,QFeatures-method",
        "logTransform,SummarizedExperiment-method",
        "normalize",
        "normalize,QFeatures-method",
        "normalize,SummarizedExperiment-method",
        "normalizeMethods",
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