Version Compatibility

Reference examples tested with: Cell Ranger 10.0+ (human/mouse refs on Ensembl v110), Seurat 5.1+, Scanpy 1.10+, scDblFinder 1.16+, SoupX 1.6+, CellBender 0.3+, harmony/scvi-tools current, ggplot2 3.5+, numpy 1.26+

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.

Note: the Cell Ranger filtered_feature_bc_matrix is cell-CALLING only, NOT ambient-corrected; recovering low-RNA cells or running SoupX/CellBender needs the RAW matrix. --include-introns is default TRUE since Cell Ranger 7 (essential for nuclei). gex_only=True/default silently drops Antibody Capture/CRISPR/HTO features. Confirm in-tool before quoting.

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.

This is a workflow skill: it owns the chaining decisions and hand-offs, not the internals of any one step. Every step below cross-references the component skill that teaches its mechanism.