GENBoostGPU

Contents

  • Quick start
    • More to explore
  • Installation
    • Prerequisites
    • CPU-only workflow (docs, linting, type checks)
    • GPU / RAPIDS workflow (full pipeline execution)
    • Next steps
  • User guide
    • Data & formats
      • Supported inputs
      • Sample and variant alignment
      • Handling missingness and QC
    • CpG pipeline
      • Overview
      • Inputs and expected files
      • Preparing inputs from BSseq
      • Running the pipeline
      • Sample alignment guidance
      • Entry points to search for
    • Workflow
      • Module responsibilities
      • Putting it together
    • Hyperparameters & tuning
      • Core boosting parameters
      • Global tuning workflow
      • Optuna integration
    • Performance & scaling
      • Execution modes
      • Memory management tips
      • Distributed execution
      • Environment checklist
    • Reproducibility
      • Random seeds
      • Deterministic settings
      • Logging & artefacts
  • Tutorials
    • Simulation tutorial
      • Setup
      • Key stages
      • Full script
      • Next steps
    • VMR caudate tutorial
      • Setup
      • Tuning and orchestration
      • Full script
      • Troubleshooting
  • API Reference
    • genboostgpu
    • genboostgpu.data_io
    • genboostgpu.enet_boosting
    • genboostgpu.hyperparams
    • genboostgpu.orchestration
    • genboostgpu.snp_processing
    • genboostgpu.tuning
    • genboostgpu.vmr_runner
  • Troubleshooting
    • CUDA / RAPIDS version mismatch
    • Out of memory (OOM)
    • Pandas / NumPy pinning conflicts
    • Dask connection issues
  • Contributing
    • Development environment
    • Running tests
    • Formatting & style
    • Issue & PR workflow
    • Adding tutorials
  • Changelog
GENBoostGPU
  • API Reference
  • View page source

API Reference

  • genboostgpu
  • genboostgpu.data_io
  • genboostgpu.enet_boosting
  • genboostgpu.hyperparams
  • genboostgpu.orchestration
  • genboostgpu.snp_processing
  • genboostgpu.tuning
  • genboostgpu.vmr_runner
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