velocycle 0.1.0.2

Bayesian model for RNA velocity estimation of periodic manifolds

VeloCycle

Manifold-constrained variational inference for RNA velocity of the cell cycle. This is the repository for the VeloCycle framework. Installation instructions and tutorials can be found below.

Getting started

Please refer to the installation instructions below as well as the tutorials contained in this repo.

Installation

You need to have Python 3.10 or newer installed.

We suggest installing VeloCycle in a separate conda environment, which for example can be created with the command:

conda create --name velocycle_env python==3.10.9

You will probably need to install git next:

conda install git

Then you can install VeloCycle using one of the following two approaches:

1. Install the latest release on PyPI:

pip install velocycle

2. Install the latest development version:

pip install git+https://github.com/lamanno-epfl/velocycle.git@main

Release notes

This is the initial release of VeloCycle corresponding to the upcoming preprint Lederer et al. 2023. These software are still under continuous development.

Contact

For questions and help requests, you can reach out to Alex Lederer and Gioele La Manno. We are happy to hear your feedback and comments! If you found a bug, please use the issue tracker.

Additional materials

For notebooks and data files not used in the tutorials included in this repo, but used in the original publication, please see the following Zenodo page and GEO.

Citation

Coming soon!