Version Compatibility

Reference examples tested with: DESeq2 1.42+, pandas 2.2+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Marker Genes and Cell Type Annotation

Find differentially expressed genes between clusters and annotate cell types.

Scanpy (Python)

Goal: Identify cluster-specific marker genes, score gene sets, and annotate cell types using Scanpy.