Cell Annotation

Version Compatibility

Reference examples assume:

• scanpy 1.10+
• celltypist 1.6+
• pandas 2.2+

Before using code patterns, verify installed versions match the environment:

• Python: python -c "import scanpy, celltypist; print(scanpy.__version__, celltypist.__version__)"
• If APIs differ, inspect the installed docs and adapt the pattern instead of retrying unchanged.

Overview

Use this skill when the user wants cluster labels or per-cell labels for scRNA-seq. The default stance is: