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  "Title": "OUTRIDER - OUTlier in RNA-Seq fInDER",
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  "Description": "Identification of aberrant gene expression in RNA-seq\ndata. Read count expectations are modeled by an autoencoder to\ncontrol for confounders in the data. Given these expectations,\nthe RNA-seq read counts are assumed to follow a negative\nbinomial distribution with a gene-specific dispersion. Outliers\nare then identified as read counts that significantly deviate\nfrom this distribution. Furthermore, OUTRIDER provides useful\nplotting functions to analyze and visualize the results.",
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  "Author": "Felix Brechtmann [aut] (ORCID: <https://orcid.org/0000-0002-0110-152X>),\nChristian Mertes [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1091-205X>),\nAgne Matuseviciute [aut],\nMichaela Fee Müller [ctb],\nAndrea Raithel [ctb],\nVicente Yepez [aut] (ORCID: <https://orcid.org/0000-0001-7916-3643>),\nJulien Gagneur [aut] (ORCID: <https://orcid.org/0000-0002-8924-8365>)",
  "Maintainer": "Christian Mertes <mertes@in.tum.de>",
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      "page": "aberrant",
      "title": "Number of aberrant events",
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        "aberrant,OutriderDataSet-method"
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      "page": "computeGeneLength",
      "title": "Extracting the gene length from annotations",
      "topics": [
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      "title": "Extracting the latent space",
      "topics": [
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      "page": "computePvalues",
      "title": "Calculate P-values",
      "topics": [
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        "computePvalues,OutriderDataSet-method"
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    {
      "page": "computeZscores",
      "title": "Z score computation",
      "topics": [
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        "computeZscores,OutriderDataSet-method"
      ]
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    {
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      "title": "Autoencoder function to correct for confounders.",
      "topics": [
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    },
    {
      "page": "counts",
      "title": "Accessors for the 'counts' slot of an OutriderDataSet object.",
      "topics": [
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        "counts,OutriderDataSet-method",
        "counts<-,OutriderDataSet,matrix-method"
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        "estimateBestQ,",
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      "title": "Filter expression",
      "topics": [
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        "filterExpression,OutriderDataSet-method"
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      "title": "Fit the negative binomial distribution",
      "topics": [
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        "fit.OutriderDataSet"
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    {
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      "title": "Calculate FPM and FPKM values",
      "topics": [
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        "getBestQ",
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      "topics": [
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        "normalizationFactors,OutriderDataSet-method",
        "normalizationFactors<-,OutriderDataSet,data.frame-method",
        "normalizationFactors<-,OutriderDataSet,DataFrame-method",
        "normalizationFactors<-,OutriderDataSet,matrix-method",
        "normalizationFactors<-,OutriderDataSet,NULL-method"
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      "page": "OUTRIDER",
      "title": "OUTRIDER - Finding expression outlier events",
      "topics": [
        "OUTRIDER"
      ]
    },
    {
      "page": "OutriderDataSet-class",
      "title": "OutriderDataSet class and constructors",
      "topics": [
        "OutriderDataSet",
        "OutriderDataSet-class"
      ]
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    {
      "page": "plotFunctions",
      "title": "Visualization functions for OUTRIDER",
      "topics": [
        "plotAberrantPerSample",
        "plotAberrantPerSample,OutriderDataSet-method",
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      "source": "OUTRIDER.Rnw",
      "filename": "OUTRIDER.pdf",
      "title": "OUTRIDER: OUTlier in RNA-seq fInDER",
      "engine": "knitr::knitr",
      "headings": [
        "1 Introduction",
        "2 Prerequisites",
        "3 A quick tour",
        "4 An OUTRIDER analysis in detail",
        "5 Results",
        "6 Additional features",
        "References"
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      "created": "2018-03-26 06:15:02",
      "modified": "2025-05-20 08:34:31",
      "commits": 32
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