theislab / Scvelo
Programming Languages
|PyPI| |PyPIDownloads| |CI|
scVelo - RNA velocity generalized through dynamical modeling
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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">
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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 ^^^^^^^^^^^^^^^^^^^^^^^^^
- estimate RNA velocity to study cellular dynamics.
- identify putative driver genes and regimes of regulatory changes.
- infer a latent time to reconstruct the temporal sequence of transcriptomic events.
- estimate reaction rates of transcription, splicing and degradation.
- use statistical tests, e.g., to detect different kinetics regimes.
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 ^^^^^^^^^^^
- Feb/2021: scVelo goes multi-core
- Dec/2020: Cover of
Nature Biotechnology <https://www.nature.com/nbt/volumes/38>
_ - Nov/2020: Talk at
Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>
_ - Oct/2020:
Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>
_ - Oct/2020: Map cell fates with
CellRank <https://cellrank.org>
_ - Sep/2020: Talk at
Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>
_ - Aug/2020:
scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>
_
Reference
^^^^^^^^^
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>
_.
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Support
^^^^^^^
Found a bug or would like to see a feature implemented? Feel free to submit an
issue <https://github.com/theislab/scvelo/issues/new/choose>
.
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 email <mailto:[email protected]>
.
Your help to improve scVelo is highly appreciated.
For further information visit scvelo.org <https://scvelo.org>
.
.. |PyPI| image:: https://img.shields.io/pypi/v/scvelo.svg :target: https://pypi.org/project/scvelo
.. |PyPIDownloads| image:: https://pepy.tech/badge/scvelo :target: https://pepy.tech/project/scvelo
.. |Docs| image:: https://readthedocs.org/projects/scvelo/badge/?version=latest :target: https://scvelo.readthedocs.io
.. |CI| image:: https://img.shields.io/github/workflow/status/theislab/scvelo/CI/master :target: https://github.com/theislab/scvelo/actions?query=workflow%3ACI
.. _scanpy: https://scanpy.readthedocs.io
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