scVelo — RNA Velocity Analysis

Overview

scVelo is the leading Python package for RNA velocity analysis in single-cell RNA-seq data. It infers cell state transitions by modeling the kinetics of mRNA splicing — using the ratio of unspliced (pre-mRNA) to spliced (mature mRNA) abundances to determine whether a gene is being upregulated or downregulated in each cell. This allows reconstruction of developmental trajectories and identification of cell fate decisions without requiring time-course data.

Installation: uv pip install "scvelo==0.3.4" (latest as of mid-2025). Gotcha: scVelo's deps declare numpy>=1.17 with no upper bound, but the stack breaks under numpy 2.x — if you hit cryptic np.float_/dtype errors on import or in plotting, pin numpy<2 (e.g. numpy==1.26.4). pandas 2.x is fine on 0.3.x.

Key resources:

• Documentation: https://scvelo.readthedocs.io/
• GitHub: https://github.com/theislab/scvelo
• Paper: Bergen et al. (2020) Nature Biotechnology. PMID: 32747759

When to Use This Skill

Use scVelo when: