Cellphonedb Skill

Comprehensive assistance with CellPhoneDB development, generated from official documentation.

When to Use This Skill

This skill should be triggered when you need to:

Data Preparation & Analysis:

• Prepare meta and counts data files for CellPhoneDB analysis
• Validate and preprocess single-cell RNA-seq data for interaction analysis
• Subsample counts data for computational efficiency
• Set up proper cell type annotations and metadata formatting

Cell-Cell Communication Analysis:

• Identify significant ligand-receptor interactions between cell types
• Perform statistical analysis of cell-type specific communication
• Analyze spatial microenvironments and neighborhood interactions
• Query and filter interaction results based on expression thresholds