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  "Title": "Identifying Genes Overexpressed in Subsets of Tumors from\nTumor-Normal mRNA Expression Data",
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  "Author": "Daniel Pique, John Greally, Jessica Mar",
  "Maintainer": "Daniel Pique <daniel.pique@med.einstein.yu.edu>",
  "Description": "This package helps identify mRNAs that are overexpressed\nin subsets of tumors relative to normal tissue. Ideal inputs\nwould be paired tumor-normal data from the same tissue from\nmany patients (>15 pairs). This unsupervised approach relies on\nthe observation that oncogenes are characteristically\noverexpressed in only a subset of tumors in the population, and\nmay help identify oncogene candidates purely based on\ndifferences in mRNA expression between previously unknown\nsubtypes.",
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    {
      "page": "exprTumIsof",
      "title": "Human Breast Cancer RNA-sequencing data from TCGA - Tumor Tissue",
      "topics": [
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    },
    {
      "page": "mixModelParams",
      "title": "Generate the parameters for two 2-component Gaussian mixture models with equal variances",
      "topics": [
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    {
      "page": "oncoMixBimodal",
      "title": "Creating a schematic of a 2-component mixture model",
      "topics": [
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    },
    {
      "page": "oncoMixIdeal",
      "title": "Creating an ideal oncomix gene",
      "topics": [
        "oncoMixIdeal"
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    },
    {
      "page": "oncoMixTraditionalDE",
      "title": "Creating a schematic of a traditional diff. expression experiment",
      "topics": [
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    {
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      "title": "Plot a histogram of gene expression values from tumor and adjacent normal tissue.",
      "topics": [
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    },
    {
      "page": "queryRes",
      "title": "Oncogene Database Mapping Gene Symbol to UCSC ID (kgID)",
      "topics": [
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    },
    {
      "page": "scatterMixPlot",
      "title": "Generate a scatter plot with the output from mixModelParams",
      "topics": [
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    {
      "page": "topGeneQuants",
      "title": "Identify genes that meet pre-specified quantiles",
      "topics": [
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      "source": "oncomix.Rmd",
      "filename": "oncomix.html",
      "title": "Oncomix Vignette",
      "author": "Daniel G. Piqué",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "1.1 Motivation for Developing Oncomix",
        "1.2 Distribution of Oncogene mRNA Expression",
        "1.3 Comparison of Oncomix to Existing Differential Expression Methods",
        "2. Identifying Oncogene Candidates",
        "2.1 Loading Example Data and Exploring the mixModelParams Object",
        "2.2 Selecting Genes that Appear Most Like the Idealized Oncogene",
        "3. Visualize the Output",
        "3.1 Visualize Isoforms with a High SI & Oncomix Score",
        "3.2 Visualize the Distribution of Isoforms that Map to Known Oncogenes",
        "3.3 Visualize the Distribution of the Oncomix Score",
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      "created": "2017-08-14 15:06:33",
      "modified": "2017-10-10 23:08:30",
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