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<a href="https://scvelo.org"> <img src="https://user-images.githubusercontent.com/31883718/67709134-a0989480-f9bd-11e9-8ae6-f6391f5d95a0.png" width="400px" align="left"> </a>
scVelo is a scalable toolkit for RNA velocity analysis in single cells, based on
Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>_.
RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
scVelo generalizes the concept of RNA velocity
La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>_)
by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
scVelo's key applications ^^^^^^^^^^^^^^^^^^^^^^^^^
scVelo has, for instance, recently been used to study immune response in COVID-19
patients and dynamic processes in human lung regeneration. Find out more in this list of
application examples <https://scholar.google.com/scholar?cites=18195185735875895912>_.
Latest news ^^^^^^^^^^^
Perspectives paper out in MSB <https://doi.org/10.15252/msb.202110282>_
Nature Biotechnology <https://www.nature.com/nbt/volumes/38>_
Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>_
Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>_
Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>_
scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>_
La Manno et al. (2018), RNA velocity of single cells,
Bergen et al. (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>_.
Bergen et al. (2021), RNA velocity - current challenges and future perspectives,
Molecular Systems Biology <https://doi.org/10.15252/msb.202110282>_.
Found a bug or would like to see a feature implemented? Feel free to submit an
Have a question or would like to start a new discussion? Head over to
GitHub discussions <https://github.com/theislab/scvelo/discussions>.
In either case, you can also always send us an
Your help to improve scVelo is highly appreciated.
For further information visit
.. |Docs| image:: https://readthedocs.org/projects/scvelo/badge/?version=latest :target: https://scvelo.readthedocs.io
.. _scanpy: https://scanpy.readthedocs.io
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