alterlab-scvelo

# 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: - **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 a pseudotime derived...