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. Complem…
---
name: scvelo
description: 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.
license: BSD-3-Clause
metadata: {"version": "1.0", "skill-author": "Kuan-lin Huang"}
---
# 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:** `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… load the full skill through Skill Me