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  • Quickstart
  • Clocks and Other Models
  • GEO Data Sources
  • DNA Methylation Array Data Standard V-2410
  • Examples
    • Omics Biomarker Examples
      • Local Data Loading
      • “Transcriptomic Clock” using GEO Data
      • “Epigenetic Clocks” in GEO Data
      • Down Syndrome Epigenetic Plotting
      • Performing custom imputations
    • Composite Biomarkers Examples
      • “Phenotypic Ages” in NHANES Data
    • Challenge Submission Examples
      • Building a competition submission using an existing model
      • Exploring the Challenge Data
      • Training an ElasticNet model
    • Deconvolution Examples
      • “Deconvolution Example”
    • Additional Visualization Examples
      • Quality control visualization using GEO datasets
      • Clock/model visualizations using GEO datasets
      • DNA methylation visualizations using GEO datasets
  • API References
    • biolearn.data_library: DataLibrary
      • biolearn.data_library.DataLibrary
      • biolearn.data_library.DataSource
      • biolearn.data_library.GeoData
    • biolearn.model_gallery: ModelGallery
      • biolearn.model_gallery.ModelGallery
    • biolearn.cache: Cache
      • biolearn.cache.NoCache
      • biolearn.cache.LocalFolderCache
    • biolearn.imputation: Data Imputation Functions
      • biolearn.imputation.impute_from_standard
      • biolearn.imputation.impute_from_average
      • biolearn.imputation.hybrid_impute
    • biolearn.mortality: Mortality Predictor Evaluation
      • biolearn.mortality.run_predictions
      • biolearn.mortality.calculate_c_index
      • biolearn.mortality.calculate_mortality_hazard_ratios
      • biolearn.mortality.calculate_age_adjusted_c_index
      • biolearn.mortality.calculate_log_rank_test
      • biolearn.mortality.plot_hazard_ratios
    • biolearn.load: Data Loading Utilities
      • biolearn.load.load_nhanes
      • biolearn.load.load_fhs

Development

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Omics Biomarker Examples#

Plots results of running omics based biomarker models functions. Includes methylation and transcriptomic data.

Local Data Loading

Local Data Loading

“Transcriptomic Clock” using GEO Data

"Transcriptomic Clock" using GEO Data

“Epigenetic Clocks” in GEO Data

"Epigenetic Clocks" in GEO Data

Down Syndrome Epigenetic Plotting

Down Syndrome Epigenetic Plotting

Performing custom imputations

Performing custom imputations
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