Instructions for Each Functional Module

• Detailed introduction to 14 functional modules, including purpose, usage, input parameter description, output result explanation, parameter tuning suggestions, and performance testing.

• The order of the 14 functional modules is: Data Processing, Cell Type Annotation, Spatial Domain Identification, Cellular Neighborhood Analysis, CNV Analysis, Spatial Gene Co-expression, Differential Gene Analysis, Gene Set Enrichment Analysis,Protein Interaction Network Analysis, Cell Communication Analysis, Trajectory Analysis, Transcription Factor Analysis, Cell-type Spatial Relationship Analysis, and Public Bulk Database Validation.