velovi

Variational inference for RNA velocity. This is an experimental repo for the veloVI model. Installation instructions and tutorials are in the docs. Over the next few months veloVI will move into scvelo.

Getting started

Please refer to the documentation.

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.

There are several alternative options to install velovi:

1. Install the latest release on PyPI:

pip install velovi

2. Install the latest development version:

pip install git+https://github.com/yoseflab/velovi.git@main

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

@article{gayoso2022deep,
  title={Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
  author={Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron M and Theis, Fabian J and Yosef, Nir},
  journal={bioRxiv},
  pages={2022--08},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}