scVelo RNA Velocity

When to use

Use for kinetic analysis of aligned spliced/unspliced RNA counts, directional trajectory hypotheses, gene-level phase portraits, and dynamical latent time. Use the model reference for assumptions, transition probabilities, and an optional CellRank handoff.

RNA velocity estimates an expression derivative under a model. Smooth arrows are not observed cell movement, lineage tracing, causal drivers, or proof of future fate. The dynamical estimator is not automatically more accurate than a steady-state estimator on every dataset.

Tested environment and compatibility

The maintained workflow targets scVelo 0.3.4, Scanpy 1.12.4, AnnData 0.13.4, NumPy 2.5.3, pandas 2.3.3, SciPy 1.18.1, Matplotlib 3.11.2, and loompy 3.0.8 on Python 3.13. Use an isolated environment: