Version Compatibility

Reference examples tested with: Cell Ranger 8.0+, 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
• CLI: <tool> --version then <tool> --help to confirm flags

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

Trajectory Inference

Monocle3 (R)

Goal: Infer developmental trajectories and pseudotime ordering using Monocle3's principal graph approach.

Approach: Learn a principal graph through the data manifold, order cells along the graph from a root state, and extract pseudotime values.