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  "Type": "Package",
  "Title": "Extract and Analyze Median Molecule Intensity from 'citrus'\nOutput",
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  "Date": "2018-07-05",
  "Author": "Allison Throm",
  "Maintainer": "Allison Throm <throm@wustl.edu>",
  "Description": "Citrus is a computational technique developed for the\nanalysis of high dimensional cytometry data sets. This package\nextracts, statistically analyzes, and visualizes marker\nexpression from 'citrus' data. This code was used to generate\ndata for Figures 3 and 4 in the forthcoming manuscript: Throm\net al. “Identification of Enhanced Interferon-Gamma Signaling\nin Polyarticular Juvenile Idiopathic Arthritis with Mass\nCytometry”, JCI-Insight. For more information on Citrus, please\nsee: Bruggner et al. (2014) <doi:10.1073/pnas.1408792111>. To\ndownload the 'citrus' package, please see\n<https://github.com/nolanlab/citrus>.",
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    "email": "throm@wustl.edu"
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    "filterMarker",
    "findclust",
    "findSig",
    "plotdif",
    "plotdif2",
    "posthoc",
    "processforanova",
    "sortmat"
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      "title": "Cytometry data set for example of Citrus data set from nolanlab/citrus",
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      "title": "Correlation data for example of Citrus data set from nolanlab/citrus",
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    {
      "page": "allmeds",
      "title": "Gets matrices of medians for each individual sample for all measured parameters for all clusters",
      "topics": [
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    },
    {
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      "title": "Clustering data for example of Citrus data set from nolanlab/citrus",
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    {
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      "title": "Correlation data for example of Citrus data set from nolanlab/citrus",
      "topics": [
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    {
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      "title": "Gets matrices of medians for each individual sample for all measured parameters for all clusters",
      "topics": [
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      ]
    },
    {
      "page": "clustermeds",
      "title": "Gets matrix of medians for desired measured features for all clusters meeting threshold requirements specified in Citrus",
      "topics": [
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      ]
    },
    {
      "page": "difMarkerPlots",
      "title": "Plot dot plots of features where both clusters are significantly different from the reference cluster without processing data before hand",
      "topics": [
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    },
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      "page": "difMarkerPlots2",
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      "topics": [
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      "title": "Filters list of data matrices with columns corresponding to the measured parameters of interest",
      "topics": [
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      ]
    },
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      "title": "Filters list to contain only desired clusters",
      "topics": [
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      "page": "findSig",
      "title": "Assesses significance of ANOVA and t-test results",
      "topics": [
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      ]
    },
    {
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      "title": "Plot dot plots of features where both clusters are significantly different from the reference cluster",
      "topics": [
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    },
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      "page": "plotdif2",
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      "topics": [
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    },
    {
      "page": "posthoc",
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      "topics": [
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    },
    {
      "page": "processforanova",
      "title": "Processes cluster signaling data in form for statistical analysis",
      "topics": [
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    },
    {
      "page": "sortmat",
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