RegVelo is an end-to-end framework to infer regulatory cellular dynamics through coupled splicing dynamics. See our RegVelo manuscript and documentation to learn more.
Feel free to open an issue if you encounter a bug, need help, have a suggestion, or notice any cases where regvelo doesn't work as expected. Reports of unexpected behavior or edge cases are especially valuable and help us continue improving the package! We also maintain an FAQ that addresses some commonly encountered questions and unexpected behaviors. You are also welcome to contact the lead developer directly: [email protected]
- Estimate RNA velocity governed by gene regulation.
- Infer latent time to indicate the cellular differentiation process.
- Estimate intrinsic and extrinsic velocity uncertainty Gayoso et al. (2024).
- Estimate regulon perturbation effects via CellRank framework (Lange et al. (2022), Weiler et al. (2024)).
We have tutorials to help you get started.
You need to have Python 3.10 or newer installed on your system.
There are several options to intall regvelo:
- Install the latest release of
regvelofrom PyPI via
pip install regvelo- Install the latest development version via
pip install git+https://github.com/theislab/regvelo.git@mainRegVelo pipeline can be run using an agentic workflow via Biomni lab, which allows user to upload custom datasets and run full analysis using a chat-based approach.
If you find RegVelo useful for your research, please consider citing our work as:
@article{wang2026regvelo,
title={RegVelo: gene-regulatory-informed dynamics of single cells},
author={Wang, Weixu and Hu, Zhiyuan and Weiler, Philipp and Mayes, Sarah and Lange, Marius and Wang, Jingye and Xue, Zhengyuan and Sauka-Spengler, Tatjana and Theis, Fabian J},
journal={Cell},
year={2026},
publisher={Elsevier},
doi={10.1016/j.cell.2026.04.022}
}