https://github.com/theislab/regvelo
inferring regulatory cellular dynamics
https://github.com/theislab/regvelo
generative-model grn-inference perturbation-analysis rna-velocity-estimation single-cell-dynamics
Last synced: 10 months ago
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inferring regulatory cellular dynamics
- Host: GitHub
- URL: https://github.com/theislab/regvelo
- Owner: theislab
- License: bsd-3-clause
- Created: 2023-02-16T00:04:56.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-09-20T13:10:28.000Z (10 months ago)
- Last Synced: 2025-09-20T14:51:33.695Z (10 months ago)
- Topics: generative-model, grn-inference, perturbation-analysis, rna-velocity-estimation, single-cell-dynamics
- Language: Python
- Homepage: https://regvelo.readthedocs.io
- Size: 70.3 MB
- Stars: 56
- Watchers: 2
- Forks: 5
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# RegVelo: gene-regulatory-informed dynamics of single cells
**RegVelo** is an end-to-end framework to infer regulatory cellular dynamics through coupled splicing dynamics.
See our [RegVelo manuscript](https://www.biorxiv.org/content/10.1101/2024.12.11.627935v1) and [documentation](https://regvelo.readthedocs.io/en/latest/index.html) to learn more.
Feel free to open an [issue](https://github.com/theislab/regvelo/issues/new) 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)](https://www.nature.com/articles/s41592-023-01994-w).
- Estimate regulon perturbation effects via CellRank framework ([Lange et al. (2022)](https://www.nature.com/articles/s41592-021-01346-6), [Weiler et al. (2024)](https://www.nature.com/articles/s41592-024-02303-9)).
## Getting started
We have [tutorials](https://regvelo.readthedocs.io/en/latest/tutorials/index.html) to help you get started.
## Installation
You need to have Python 3.10 or newer installed on your system.
There are several options to intall regvelo:
1. Install the latest release of `regvelo` from PyPI via
```bash
pip install regvelo
```
2. Install the latest development version via
```bash
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}
}
```