Metadata-Version: 2.4
Name: regvelo
Version: 0.3.0
Summary: Estimation of RNA velocity with variational inference.
Author-email: Weixu Wang <weixu.wang@helmholtz-munich.de>
License: BSD-3-Clause
Project-URL: documentation, https://regvelo.readthedocs.io/
Project-URL: source, https://github.com/theislab/regvelo
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Natural Language :: English
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata>=0.10.8
Requires-Dist: scanpy>=1.10.3
Requires-Dist: scvelo>=0.3.2
Requires-Dist: scvi-tools<1.2.1,>=1.0.0
Requires-Dist: scikit-learn>=0.21.2
Requires-Dist: velovi>=0.3.1
Requires-Dist: torchode>=0.1.6
Requires-Dist: cellrank>=2.0.0
Requires-Dist: matplotlib>=3.7.3
Requires-Dist: pandas>=2.0.3
Requires-Dist: seaborn>=0.13.2
Requires-Dist: numpy>=1.25.2
Requires-Dist: scipy<1.16.0,>=1.11.1
Requires-Dist: torch<2.6.0
Requires-Dist: rich>=10.0.0
Provides-Extra: dev
Requires-Dist: black>=20.8b1; extra == "dev"
Requires-Dist: pytest>=4.4; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: codecov>=2.0.8; extra == "dev"
Requires-Dist: scanpy; extra == "dev"
Requires-Dist: loompy; extra == "dev"
Requires-Dist: jupyter; extra == "dev"
Requires-Dist: pre-commit>=2.7.1; extra == "dev"
Provides-Extra: docs
Requires-Dist: sphinx>=4.1; extra == "docs"
Requires-Dist: furo>=2022.09.29; extra == "docs"
Requires-Dist: scanpydoc>=0.5; extra == "docs"
Requires-Dist: ipython>=7.1.1; extra == "docs"
Requires-Dist: myst-nb; extra == "docs"
Requires-Dist: sphinx-book-theme>=1.0.0; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Requires-Dist: sphinxcontrib-bibtex==2.6.3; extra == "docs"
Requires-Dist: ipykernel; extra == "docs"
Requires-Dist: sphinx_design>=0.3.0; extra == "docs"
Requires-Dist: sphinx_autodoc_typehints>=1.10.3; extra == "docs"
Provides-Extra: tutorials
Requires-Dist: scanpy; extra == "tutorials"
Requires-Dist: matplotlib; extra == "tutorials"
Dynamic: license-file

# RegVelo: gene-regulatory-informed dynamics of single cells

<img src="https://github.com/theislab/regvelo/blob/main/docs/_static/img/overview_fig.png?raw=true" alt="RegVelo" width="600" />

**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. Since `regvelo` is not on PyPI yet, please use option-2 for now to install.

There are several options to intall regvelo:

1. Install the latest release of `regvelo` from PyPI (TODO) 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}
  }
```

