easydecon

Getting started

  • Installation and quickstart
  • How easydecon works
  • Marker inputs and table schema

Core workflow

  • Phase 1: marker-expression priors
  • Phase 2: marker-profile similarity
  • UCell-like Phase 2 scoring
  • Understanding EasyDeconResult

Marker preparation

  • Reusing marker preparation
  • Scanpy markers
  • Reference-profile markers
  • Marker roles and phase-specific routing

Advanced workflows

  • Refining broad groups into subclusters
  • Optional Phase 2 candidate pruning
  • Spatial niche detection
  • Visualizing easydecon results

Validation and reference

  • Synthetic validation
  • Optional bin2cell segmentation helper
  • Troubleshooting
  • Glossary
  • API reference
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