RegVelo: gene-regulatory-informed dynamics of single cells

RegVelo

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 our help or just want to make a comment/suggestion.

RegVelo's key applications

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)).

Getting started

We have tutorials to help you get started.

Installation

You need to have Python 3.10 or newer installed on your system. Since regvelo is not on PyPI yet, please use option-2 for now to install.

There are several options to intall regvelo:

Install the latest release of regvelo from PyPI (TODO) via

  pip install regvelo

Install the latest development version via

  pip install git+https://github.com/theislab/regvelo.git@main

Citation

If you find RegVelo useful for your research, please consider citing our work as:

  @article{wang2024regvelo,
    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={bioRxiv},
    pages={2024--12},
    year={2024},
    publisher={Cold Spring Harbor Laboratory}
  }