Velocity package

This velocity analysis package provides functions for velocity analyis from single-cell RNA data. We introduce two methods, along with revised processing and visualisation functions.

• In $\kappa$-velo, we solve for the gene-wise reaction rate parameters to recover the high-dimensional velocity vector. We also present a new visualisation method to faithfully represents the velocities on low-dimensional embeddings.
• In eco-velo, by simply taking the unspliced counts as a proxy of a cell’s future state we estimates cell state velocities directly in the high-dimensional gene space.

The tools in this package are compatible with scanpy.

Instalation

To install the package from GitHub, please use:

 git clone https://github.com/HaghverdiLab/velocity_package
 cd velocity_package
 pip install -e .

How to run

Tutorials explaining the RNA analysis workflow with $\kappa$-velo and eco-velo can be found here.

References

Valérie Marot-Lassauzaie, Brigitte Joanne Bouman, et al. Towards reliable quantification of cell state velocities bioRxiv (2022)

Support

If you found a bug, would like to see a feature implemented, or have a question please open an issue.