scvelo
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
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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:
uv venv --python 3.13 .venv-velocity
uv pip install --python .venv-velocity/bin/python \
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 loompy==3.0.8
The packages above were resolved from cache and tested in an isolated uv
environment; shell paths above use POSIX syntax. Installation requires network
access unless packages are cached. No API key is required.
- Deterministic and dynamical models: native synthetic fitting, graphs, relative times, plots and H5AD round trips are tested on this stack.
- Stochastic model: scVelo 0.3.4's default GLS scalar assignment fails with
NumPy 2. Scanpy 1.12 requires NumPy 2, so installing
numpy<2beside current Scanpy is not a solution. A separately validated legacy Scanpy/NumPy environment is required; that legacy stack was not executed in this review. The helper rejects this combination before modifying data, without changing the model. - pandas 3: scVelo 0.3.4 dynamical fitting and some plots use operations no longer supported by pandas 3. Keep the explicit pandas pin.
- The upstream stable tutorial still contains removed
scv.readand older preprocessing calls. Check the 0.3.4 source when a tutorial disagrees with the installed API.