SyNG-BTS

Getting Started

  • Usage Guide
    • Installation
      • From PyPI (Recommended)
      • From Source
      • Optional Dependencies
    • Quick Start
      • Basic Import
      • Browse Bundled Datasets
      • Load TCGA Cohorts
      • Generate Synthetic Data
      • Run a Pilot Study
      • Use DataFrame Input
      • Evaluate Results
      • Sample-Size Evaluation (SyntheSize)
    • Next Steps
  • Migration Guide / Changelog
    • Function Renames
    • Parameter Changes
    • Data Input
    • Output Handling
    • Plotting
    • Evaluation Functions
    • Quick Migration Checklist
    • Changes in v3.1
      • v3.1 Quick Migration Checklist
    • Changes in v3.2
      • v3.2 Migration Checklist

User Guide

  • Synthetic Data Generation
    • Overview
    • generate
      • Examples
    • pilot_study
      • Examples
    • transfer
      • Examples
    • Choosing a Model
  • Evaluation Functions
    • Overview
    • Result Object Plotting
    • Heatmap Evaluation
      • Examples
    • UMAP Visualization
      • Examples
    • Comprehensive Evaluation
      • Example
    • Evaluation Workflow
  • Sample-Size Evaluation (SyntheSize)
    • Background
    • Quick Start
      • Evaluate a DataFrame
      • Evaluate a SyngResult
    • Workflow
    • Available Classifiers
    • Metrics
    • Log Transform
    • Verbosity
    • Sample-Size Shortcuts
    • API Reference
  • TCGA Datasets
    • Overview
    • Quick Start
    • Data layout
    • Available Datasets
    • Working with TCGADataset
      • real() and synth() return tuples
      • Reaching the underlying Subset for metadata
      • Choosing a normalization
      • Choosing a synthetic model
    • Caching and Offline Use
      • Cache location
      • Custom cache directory
      • First-call download semantics
      • Force redownload and cleanup
    • Advanced
      • Custom manifest URL
      • Dataset versioning
      • Errors users may see
    • See also
      • TCGA Quick Start
        • Loading a cohort
        • Inspecting the real data
        • Loading synthetic samples
        • Quick visual check — UMAP
        • Cache management
  • Example Datasets
    • Overview
    • Loading Datasets
    • Available Datasets
      • Example Datasets
      • Transfer Learning Datasets
      • BRCA Subtype Case Study
      • SyntheSize Evaluation Datasets
      • LIHC Subtype Case Study
    • Usage Examples
      • Case Study with BRCA Subtype
    • Using Custom Datasets
    • Data Source
  • Configuration Reference
    • Available Models
    • Common Parameters
      • Data Parameters
      • Training Parameters
      • Generation Parameters
      • Augmentation Parameters
      • Advanced Parameters (generate only)
      • Model Architecture Parameters
    • generate() Parameters
    • pilot_study() Parameters
    • transfer() Parameters
    • Output and Saving
    • Bundled Datasets

Reference

  • API Reference
    • Experiment Functions
      • generate
        • generate()
      • pilot_study
        • pilot_study()
      • transfer
        • transfer()
    • Result Objects
      • SyngResult
        • SyngResult
      • PilotResult
    • Evaluation Functions
      • heatmap_eval
        • heatmap_eval()
      • UMAP_eval
        • UMAP_eval()
      • evaluation
        • evaluation()
    • Sample-Size Evaluation (SyntheSize)
      • evaluate_sample_sizes
        • evaluate_sample_sizes()
      • plot_sample_sizes
        • plot_sample_sizes()
    • Data Utilities
      • resolve_data
        • resolve_data()
      • list_bundled_datasets
        • list_bundled_datasets()
    • TCGA Datasets
      • load_tcga_dataset
        • load_tcga_dataset()
      • list_tcga_datasets
        • list_tcga_datasets()
      • tcga_cache_dir
        • tcga_cache_dir()
      • clear_tcga_cache
        • clear_tcga_cache()
      • TCGADataset
        • TCGADataset
      • Subset
    • Model Classes
      • AE (Autoencoder)
        • AE
      • VAE (Variational Autoencoder)
        • VAE
      • CVAE (Conditional VAE)
        • CVAE
      • GAN (Generative Adversarial Network)
        • GAN
    • Package Information
      • syng_bts.__version__
      • syng_bts.__author__
      • syng_bts.__license__
SyNG-BTS
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