{
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  "Package": "scp",
  "Title": "Mass Spectrometry-Based Single-Cell Proteomics Data Analysis",
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  "Authors@R": "c(person(\"Christophe\", \"Vanderaa\",\nemail = \"vanderaa.christophe@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7443-5427\"),\nrole = c(\"aut\", \"cre\")),\nperson(\"Laurent\", \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = \"aut\"),\nperson(\"Léopold\", \"Guyot\", role = \"ctb\"))",
  "Description": "Utility functions for manipulating, processing, and\nanalyzing mass spectrometry-based single-cell proteomics data.\nThe package is an extension to the 'QFeatures' package and\nrelies on 'SingleCellExpirement' to enable single-cell\nproteomics analyses. The package offers the user the\nfunctionality to process quantitative table (as generated by\nMaxQuant, Proteome Discoverer, and more) into data tables ready\nfor downstream analysis and data visualization.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
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  "biocViews": "GeneExpression, Proteomics, SingleCell, MassSpectrometry,\nPreprocessing, CellBasedAssays",
  "BugReports": "https://github.com/UCLouvain-CBIO/scp/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:00 UTC",
  "RemoteUrl": "https://github.com/bioc/scp",
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  "Author": "Christophe Vanderaa [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7443-5427>),\nLaurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>),\nLéopold Guyot [ctb]",
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  "_published": "2026-05-30T15:04:07.492Z",
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    "cumulativeSensitivityCurve",
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    "medianCVperCell",
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    "scpModelNames",
    "scpModelResiduals",
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    "scpRemoveBatchEffect",
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    "scpVariancePlot",
    "scpVolcanoPlot"
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      "fields": [],
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      "tojson": false
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      "title": "Add scplainer Component Analysis Results",
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      "page": "aggregateFeaturesOverAssays-deprecated",
      "title": "Aggregate features over multiple assays",
      "topics": [
        "aggregateFeaturesOverAssays",
        "aggregateFeaturesOverAssays-deprecated"
      ]
    },
    {
      "page": "computeSCR",
      "title": "Compute the sample over carrier ratio (SCR)",
      "topics": [
        "computeSCR"
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    },
    {
      "page": "cumulativeSensitivityCurve",
      "title": "Cumulative sensitivity curve",
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        "predictSensitivity"
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    },
    {
      "page": "divideByReference",
      "title": "Divide assay columns by a reference column",
      "topics": [
        "divideByReference"
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    },
    {
      "page": "jaccardIndex",
      "title": "Compute the pairwise Jaccard index",
      "topics": [
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    {
      "page": "leduc_minimal",
      "title": "Minimally processed single-cell proteomics data set",
      "topics": [
        "leduc_minimal"
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    },
    {
      "page": "medianCVperCell",
      "title": "Compute the median coefficient of variation (CV) per cell",
      "topics": [
        "medianCVperCell"
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    },
    {
      "page": "mqScpData",
      "title": "Example MaxQuant/SCoPE2 output",
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    },
    {
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      "title": "Normalize single-cell proteomics (SCP) data",
      "topics": [
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    },
    {
      "page": "pep2qvalue",
      "title": "Compute q-values",
      "topics": [
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      ]
    },
    {
      "page": "readSCP",
      "title": "Read single-cell proteomics tabular data",
      "topics": [
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        "readSCPfromDIANN",
        "readSingleCellExperiment"
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    },
    {
      "page": "reportMissingValues",
      "title": "Four metrics to report missing values",
      "topics": [
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    },
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      "topics": [
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      ]
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      "page": "scp1",
      "title": "Single Cell QFeatures data",
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        "scp1"
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    },
    {
      "page": "scpAnnotateResults",
      "title": "Annotate single-cell proteomics analysis output",
      "topics": [
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    },
    {
      "page": "scplainer",
      "title": "scplainer: linear models to understand mass spectrometry-based single-cell proteomics data",
      "topics": [
        "scplainer"
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    },
    {
      "page": "ScpModel-class",
      "title": "Class to store the results of single-cell proteomics modelling",
      "topics": [
        "class:ScpModel",
        "ScpModel",
        "ScpModel-class",
        "scpModelEffects",
        "scpModelFilterNPRatio",
        "scpModelFilterThreshold",
        "scpModelFilterThreshold<-",
        "scpModelFormula",
        "scpModelInput",
        "scpModelNames",
        "scpModelResiduals"
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    },
    {
      "page": "ScpModel-DataCorrection",
      "title": "Correct single-cell proteomics data",
      "topics": [
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        "ScpModel-DataCorrection",
        "scpRemoveBatchEffect"
      ]
    },
    {
      "page": "ScpModel-DifferentialAnalysis",
      "title": "Differential abundance analysis for single-cell proteomics",
      "topics": [
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        "scpDifferentialAnalysis",
        "ScpModel-DifferentialAnalysis",
        "scpVolcanoPlot"
      ]
    },
    {
      "page": "ScpModel-VarianceAnalysis",
      "title": "Analysis of variance for single-cell proteomics",
      "topics": [
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        "scpVarianceAggregate",
        "scpVarianceAnalysis",
        "scpVariancePlot"
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    {
      "page": "ScpModel-Workflow",
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