Version Compatibility

Reference examples tested with: Cell Ranger 8.0+, ggplot2 3.5+, numpy 1.26+, 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.

Single-Cell RNA-seq Pipeline

"Analyze my single-cell RNA-seq data from counts to cell types" → Orchestrate QC filtering, normalization (scanpy/Seurat), batch integration (scVI/Harmony), clustering, marker detection, cell type annotation, and trajectory inference.

Complete workflow from 10X Genomics Cell Ranger output to annotated cell types.

Workflow Overview