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https://github.com/pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱
https://github.com/pinellolab/pyrovelocity

cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics

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𝒫robabilistic modeling of RNA velocity ⬱

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# Pyro-Velocity







Pyro-Velocity logo




𝒫robabilistic modeling of RNA velocity ⬱



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| CI/CD   | [![CID][cid-badge]][cid-link] [![codecov][codecov-badge]][codecov-link] [![pre-commit.ci status][precommit-badge]][precommit-link]               |

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| Package | [![PyPI - Version][pypi-badge]][pypi-link] [![Conda-forge badge][conda-forge-badge]][anaconda-link] [![Docker image][docker-badge]][docker-link] |

| Meta    | [![pyro-ppl-badge]][pyro-ppl-link] [![flyte-badge]][flyte-link] [![hydra-zen-badge]][hydra-zen-link] [![scvi-tools-badge]][scvi-tools-link]      |

|         | [![bear-badge]][bear-link] [![black-badge]][black-link] [![License][license-badge]][license-link] [![Tuple][tuple-badge]][tuple-link]            |



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[flyte-link]: https://docs.flyte.org

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[hydra-zen-link]: https://mit-ll-responsible-ai.github.io/hydra-zen/

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[cloudflare-link]: https://docs.pyrovelocity.net

[preprint-badge]: https://img.shields.io/badge/doi-10.1101/2022.09.12.507691v2-B31B1B

[preprint-link]: https://doi.org/10.1101/2022.09.12.507691

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[anaconda-link]: https://anaconda.org/conda-forge/pyrovelocity

[docker-badge]: https://img.shields.io/badge/docker-image-blue?logo=docker

[docker-link]: https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity

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[pyro-ppl-link]: https://pyro.ai

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[tuple-link]: https://tuple.app/github-badge






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[Pyro-Velocity](https://docs.pyrovelocity.net) is a library for probabilistic inference in minimal models approximating gene expression dynamics from, possibly multimodal, single-cell sequencing data.

It provides posterior estimates of gene expression parameters, predictive estimates of gene expression states, and local estimates of cell state transition probabilities.

It can be used as a component in frameworks that attempt to retain the ability to propagate uncertainty in predicting: distributions over cell fates from subpopulations of cell states, response to cell state perturbations, or candidate genes or gene modules that correlate with determination of specific cell fates.



---



## Documentation 📒



Please see the [Documentation](https://docs.pyrovelocity.net).



## Changelog 🔀



Changes for each release are listed in the [Changelog](https://docs.pyrovelocity.net/about/changelog).



## Contributing ✨



Please review the [Contributing Guide](https://docs.pyrovelocity.net/about/contributing) for instructions on setting up a development environment and submitting pull requests.



## Community 🏘



If you would like to apply [Pyro-Velocity](https://docs.pyrovelocity.net) in your research, have an idea for a new feature, have a problem using the library, or just want to chat, please feel free to [start a discussion](https://github.com/pinellolab/pyrovelocity/discussions).



If you have a feature request or issue using Pyro-Velocity that may require making changes to the contents of this repository, please [file an issue](https://github.com/pinellolab/pyrovelocity/issues) containing



- a [GitHub permananent link](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/creating-a-permanent-link-to-a-code-snippet) to the location in the repository you think is causing a problem or will require changes, and

- provide a [minimal reproducible example](https://en.wikipedia.org/wiki/Minimal_reproducible_example) of the problem or proposed improvement.



We are always interested in discussions and issues that can help to improve the [Documentation](https://docs.pyrovelocity.net).



## License ⚖️



[AGPL](https://github.com/pinellolab/pyrovelocity/blob/main/LICENSE)