Version Compatibility

Reference examples tested with: pertpy 0.9+, scanpy 1.10+, anndata 0.10+, sceptre 0.10+

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.

Perturb-seq Analysis

"Analyze my Perturb-seq CRISPR screen" -> Assign guides, remove cells that received a guide but were not perturbed, test each perturbation with a calibrated method, and separate "moves cells" from "changes cells".

• Python: pertpy.pp.GuideAssignment, pertpy.tl.Mixscape, pertpy.tl.Distance/DistanceTest, pertpy.tl.Milo/Sccoda
• R: sceptre (conditional-resampling test), Seurat Mixscape, scMAGeCK

Governing Principle