CellChat-Pkg-Local-Complete Skill

Comprehensive assistance with CellChat package for cell-cell communication analysis, generated from official documentation and source code.

When to Use This Skill

This skill should be triggered when:

Data Preparation & Object Creation:

• Converting single-cell data from Seurat, SingleCellExperiment, or AnnData objects to CellChat
• Preparing normalized expression matrices and cell metadata for CellChat analysis
• Setting up CellChat objects from different data formats (count matrices, spatial data)
• Handling data input issues from Python/Scanpy or other single-cell tools

Cell-Cell Communication Analysis:

• Inferring ligand-receptor interactions and signaling pathways
• Computing communication probabilities and network analysis
• Analyzing spatially resolved cell-cell communication
• Performing comparative analysis across conditions or time points