README.md

RegVelo: gene-regulatory-informed dynamics of single cells

RegVelo is a end-to-end framework to infer regulatory cellular dynamics through coupled splicing dynamics. See our RegVelo manuscript to learn more. If you use our tool in your own work, please cite it as

@article{wang:24,
    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 Theis, Fabian J.},
    doi = {10.1101/2024.12.11.627935},
    url = {https://doi.org/10.1101/2024.12.11.627935},
    year = {2024},
    publisher = {Cold Spring Harbor Laboratory},
}

Getting started

Please refer to the Tutorials

Installation

You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing Miniconda.

To create and activate a new environment

conda create -n regvelo-py310 python=3.10 --yes && conda activate regvelo-py310

Next, install the package with

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