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  "Title": "Combinatorial Polyfunctionality Analysis of Single Cells",
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  "Date": "2014-07-11",
  "Author": "Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)",
  "Authors@R": "c( person(\"Lynn\", \"Lin\", role=\"aut\", email=\"llin@fhcrc.org\"),\nperson(\"Kevin\", \"Ushey\", role=\"aut\", email=\"kushey@fhcrc.org\"),\nperson(\"Greg\", \"Finak\", role=c(\"aut\",\"cre\"), email=\"gfinak@fhcrc.org\"),\nperson(\"Raivo\", \"Kolde\", role=\"ctb\", email=\"rkolde@gmail.com\",\ncomment=\"Author of 'pheatmap', which was modified and now used internally\nin COMPASS\") )",
  "Description": "COMPASS is a statistical framework that enables unbiased\nanalysis of antigen-specific T-cell subsets. COMPASS uses a\nBayesian hierarchical framework to model all observed\ncell-subsets and select the most likely to be antigen-specific\nwhile regularizing the small cell counts that often arise in\nmulti-parameter space. The model provides a posterior\nprobability of specificity for each cell subset and each\nsample, which can be used to profile a subject's immune\nresponse to external stimuli such as infection or vaccination.",
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      "title": "COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells)",
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      "title": "Categories",
      "topics": [
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    },
    {
      "page": "CellCounts",
      "title": "Compute Number of Cells Positive for Certain Cytokine Combinations",
      "topics": [
        "CellCounts"
      ]
    },
    {
      "page": "Combinations",
      "title": "Generate Combinations",
      "topics": [
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    },
    {
      "page": "COMPASS",
      "title": "Fit the COMPASS Model",
      "topics": [
        "COMPASS"
      ]
    },
    {
      "page": "COMPASSContainer",
      "title": "Generate the Data Object used by COMPASS",
      "topics": [
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    },
    {
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      "title": "Simulated COMPASSContainer",
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        "COMPASSContainer-data"
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    },
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        "COMPASSDescription<-"
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      "title": "COMPASSResult Accessors",
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        "MeanGamma"
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      "title": "Simulated COMPASS fit",
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        "CR"
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        "plot.COMPASSResult"
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      "title": "Plot multiple COMPASSResults",
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        "Purpose",
        "Prerequisites",
        "Using SimpleCOMPASS",
        "Reading tabular ICS data",
        "Formatting the data",
        "Preparation",
        "Step 1. Separate the metadata and count data",
        "2. Split the count matrix into stimulated and non-stimulated counts.",
        "3. A Unique Sample Specific Identifier",
        "4. Name and order rows of all the matrices.",
        "5. Reformat cell population names.",
        "6. Last column should be the all-negative boolean combination.",
        "Fit a COMPASS model",
        "Visualization of results",
        "References"
      ],
      "created": "2018-03-06 15:43:30",
      "modified": "2020-05-12 18:30:40",
      "commits": 5
    }
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