Description
scvelo is an agent skill for RNA velocity analysis with scVelo, which works from spliced and unspliced single-cell RNA counts. It fits deterministic or dynamical models, examines gene phase portraits and estimates dynamical latent time. Use it for kinetic analysis of aligned counts, for directional trajectory hypotheses, and for gene-level phase portraits. For model assumptions, transition probabilities and an optional handoff to CellRank, the skill points to a model reference. The skill is careful about what RNA velocity means. It estimates an expression derivative under a model. Smooth arrows are not observed cell movement, lineage tracing, causal drivers or proof of a cell's future fate. The dynamical estimator is not automatically more accurate than the steady-state estimator on every dataset. The maintained workflow targets scVelo 0.3.4, with 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, and the skill advises an isolated environment. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- Deterministic and dynamical velocity models
- Gene phase portraits
- Dynamical latent time
- CellRank handoff option
- Targets scVelo 0.3.4
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scvelo FAQ
What does RNA velocity estimate?
An expression derivative under a model, using spliced and unspliced counts.
Do the arrows show where cells will go?
No. The skill says they are not observed movement, lineage tracing, causal drivers or proof of fate.
Is the dynamical model always better?
No. The skill says it is not automatically more accurate than the steady-state estimator on every dataset.
Which versions are targeted?
scVelo 0.3.4 with Scanpy 1.12.4 and AnnData 0.13.4, on Python 3.13.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill scvelo.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best scvelo alternatives?
Popular alternatives to scvelo include anndata, arboreto and scanpy. See all scvelo alternatives