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
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:
- Trajectory inference from snapshot data: Determine which direction cells are differentiating
- Cell fate prediction: Identify progenitor cells and their downstream fates
- Driver gene identification: Find genes whose dynamics best explain observed trajectories
- Developmental biology: Model hematopoiesis, neurogenesis, epithelial-to-mesenchymal transitions
- Latent time estimation: Order cells along…
