Cellcharter-Local Skill

Comprehensive assistance with CellCharter spatial clustering and analysis for spatial omics data.

When to Use This Skill

This skill should be triggered when:

Working with spatial omics data - spatial transcriptomics, proteomics, epigenomics, or multiomics data
Performing spatial clustering - identifying cellular niches and spatial domains
Analyzing neighborhood relationships - computing enrichment, proximity, and spatial interactions
Characterizing spatial domains - calculating shape metrics, boundaries, and domain properties
Comparing spatial conditions - differential analysis between disease vs normal states
Processing large spatial datasets - scaling to millions of cells with GPU acceleration
Implementing spatial preprocessing - dimensionality reduction with scVI/scArches
Visualizing spatial results - plotting boundaries, enrichment, and spatial scatter plots
Learning spatial analysis methods - understanding best practices for spatial domain identification
Debugging spatial analysis workflows - troubleshooting clustering and neighborhood analysis