MethylSeg Documentation

methylseg is the reusable methylation segmentation package in this repository. Start with the README to train a model from WGBS or TCGA HM450K data. The API reference and example notebooks provide advanced workflows.

Documentation

Contents

• MethylSeg
  • Hardware requirements
  • Installation
  • Reference files
  • Quickstart
  • Input formats
  • Outputs
  • Citation
  • Planned support
  • Reporting issues
  • License
• MethylSeg Methodology
  • Workflow at a glance
  • 1. Data preprocessing
  • 2. Context-aware emission generation
  • 3. CpG state assignment
  • 4. HMM-based smoothing
  • 5. Region cleaning
  • Implementation reference
• Methylome Segmentation Workflow
  • Workflow layers
  • Sample preparation
  • Fitting state assignment
  • Segmentation and cleaning
  • What run_pathway() calls
  • Alternative usage patterns
  • Related guides
• Plotting MethylSeg Results
  • Pathway-level plotting
  • Assigner diagnostics
  • Analyzer and segmentor diagnostics
  • Custom colors and overlays
  • Choosing a plotting layer
• Example Notebooks
  • Quickstart
  • Run the Full MethylSeg Pipeline
  • KMeans-Based Model Example
  • Rule-Based Model Example
  • MethylSeg Components Example
  • Saving a MethylSeg Model
  • MethylSeg Plotting Gallery
• API Reference
  • Workflow objects
  • Enums and labels
  • HMM backends
  • Utility helpers
  • Advanced utilities and constants
• Troubleshooting
  • LLVM crash on ARM64 systems
• MethylSeg Roadmap
  • 1.1.0
  • 1.2.0
  • 2.0.0