Version Compatibility

Reference examples tested with: scanpy 1.10+, scVelo 0.3+, CellRank 2.0+, Monocle3 1.3+, Slingshot 2.x

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

"Find the developmental trajectory in my data" -> Order cells along a continuous manifold and assign a pseudotime, fate probabilities, or velocity direction.

• Python: sc.tl.paga/sc.tl.dpt (scanpy), palantir, scvelo, cellrank (kernels + GPCCA)
• R: slingshot, monocle3, tradeSeq

Governing Principle