Cells

This subpackage contains functions to annotate and assess cell annotation.

Table of Contents

• De Novo
  • Annotation by marker genes
  • Annotation by marker genes (in the context of the other marker genes)
  • Annotation based on expected cell types
  • Automatically calculate cell type gene module scores
  • Annotate groups of cells by Biological Process
  • Automatically determine (Leiden) clustering resolution
  • Core Functions
• Transfer Labels
  • Using an sklearn classifier
  • Based on harmony integration
• Benchmark
  • AI compare cell type labels
  • Calculate label agreement metrics
  • Utility functions
• Error Correction