{
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  "Package": "EpiMix",
  "Title": "EpiMix: an integrative tool for the population-level analysis of\nDNA methylation",
  "Version": "1.15.0",
  "Description": "EpiMix is a comprehensive tool for the integrative\nanalysis of high-throughput DNA methylation data and gene\nexpression data. EpiMix enables automated data downloading\n(from TCGA or GEO), preprocessing, methylation modeling,\ninteractive visualization and functional annotation.To identify\nhypo- or hypermethylated CpG sites across physiological or\npathological conditions, EpiMix uses a beta mixture modeling to\nidentify the methylation states of each CpG probe and compares\nthe methylation of the experimental group to the control\ngroup.The output from EpiMix is the functional DNA methylation\nthat is predictive of gene expression. EpiMix incorporates\nspecialized algorithms to identify functional DNA methylation\nat various genetic elements, including proximal cis-regulatory\nelements of protein-coding genes, distal enhancers, and genes\nencoding microRNAs and lncRNAs.",
  "Authors@R": "c(\nperson(\"Yuanning\", \"Zheng\", email = c(\"eric2021@stanford.edu\"), role = c(\"aut\", \"cre\")),\nperson(\"Markus\", \"Sujansky\", email = c(\"sujansky@bc.edu\"), role = c(\"aut\")),\nperson(\"John\", \"Jun\", email = c(\"johnjun094@gmail.com\"), role = c(\"aut\")),\nperson(\"Olivier\", \"Gevaert\", email = c(\"ogevaert@stanford.edu\"), role = c(\"aut\"))\n)",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "biocViews": "Software, Epigenetics, Preprocessing, DNAMethylation,\nGeneExpression, DifferentialMethylation",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/gevaertlab/EpiMix/issues",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:39 UTC",
  "RemoteUrl": "https://github.com/bioc/EpiMix",
  "RemoteRef": "HEAD",
  "RemoteSha": "11cb6d5ef972fd044a3dfdd06bac7d766d3e0394",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:46:20 UTC",
    "User": "root"
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  "Author": "Yuanning Zheng [aut, cre],\nMarkus Sujansky [aut],\nJohn Jun [aut],\nOlivier Gevaert [aut]",
  "Maintainer": "Yuanning Zheng <eric2021@stanford.edu>",
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      "page": "dot-extractPriMiRNA",
      "title": "The extractPriMiRNA function",
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      ]
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    {
      "page": "addDistNearestTSS",
      "title": "Calculate the distance between probe and gene TSS",
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      ]
    },
    {
      "page": "addGeneNames",
      "title": "The addGeneNames function",
      "topics": [
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    },
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      "title": "Calculate distance from region to nearest TSS",
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      "title": "The ClusterProbes function",
      "topics": [
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    {
      "page": "EpiMix",
      "title": "The EpiMix function",
      "topics": [
        "EpiMix"
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    {
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      "title": "The EpiMix_getInfiniumAnnotation function",
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      "title": "The EpiMix_PlotGene function",
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      "title": "The EpiMix_PlotModel function.",
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      "title": "The EpiMix_PlotProbe function",
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      "title": "EpiMix_PlotSurvival function",
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      "title": "The filterProbes function",
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      "title": "The find_miRNA_targets function",
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      "title": "The functionEnrich function",
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      "title": "The generateFunctionalPairs function",
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      "title": "The GEO_Download_DNAmethylation function",
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      "title": "the GEO_getSampleMap function",
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      "title": "Calculate empirical Pvalue",
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      "title": "The getMethStates_Helper function",
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      "title": "GetNearGenes to collect nearby genes for one locus.",
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      "title": "The GetSurvivalProbe function",
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      "title": "getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.",
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      "page": "MethylMix_Predict",
      "title": "The MethylMix_Predict function",
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      "title": "The predictOneGene function",
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      "title": "The Preprocess_DNAMethylation function",
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      "title": "The Preprocess_GeneExpression function",
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      "page": "removeDuplicatedGenes",
      "title": "The removeDuplicatedGenes function",
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      "page": "TCGA_Select_Dataset",
      "title": "The TCGA_Select_Dataset function",
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      "page": "translateMethylMixResults",
      "title": "The translateMethylMixResults function",
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      "page": "validEpigenomes",
      "title": "The validEpigenomes function",
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      "filename": "Methylation_Modeling.html",
      "title": "EpiMix",
      "author": "| Yuanning Zheng, John Jun, Kevin Brennan and Olivier Gevaert | | Stanford Center for Biomedical Informatics Research (BIMR) | Department of Medicine | 1265 Welch Road | Stanford CA, 94305-5479",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Installation",
        "2.1 Bioconductor",
        "2.2 Github",
        "3. Data input",
        "4. Methylation modeling",
        "4.1 Regular mode",
        "4.2 Enhancer mode",
        "4.3 miRNA mode",
        "4.4 lncRNA mode",
        "5. One-step functions for TCGA data",
        "6. Step-by-step functions for TCGA data",
        "6.1 Download and preprocess DNA methylation data from TCGA",
        "6.2 Download and preprocess gene expression data",
        "7. Visualization",
        "7.1 Mixture model and gene expression",
        "7.2 Genome-browser style visualization",
        "7.2.1 Integrative visualization of the chromatin state, DNA methylation, and transcript structure of a specific gene",
        "7.2.2 Plot the chromatin state of a CpG site and the expression of its nearby genes",
        "8. Pathway enrichment analysis",
        "8.1 Gene ontology (GO) analysis",
        "8.2 KEGG pathway enrichment analysis",
        "9. Biomarker identification",
        "10. Find potential miRNA targets",
        "11. Session Information"
      ],
      "created": "2022-06-02 22:09:30",
      "modified": "2023-07-11 04:22:26",
      "commits": 6
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "epimix",
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