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Projects"],"sub_categories":["Iterative"],"readme":"# Pyro-Velocity\n\n\u003cdiv align=\"center\" style=\"margin-left: auto; margin-right: auto; max-width: 540px; overflow-x: auto;\"\u003e\n\u003ca href=\"https://docs.pyrovelocity.net\"\u003e\n\u003cimg\n    src=\"https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/_static/logo.png\"\n    alt=\"Pyro-Velocity logo\"\n    style=\"width: 300px; max-width: 60%; height: auto; max-height: 350px;\"\n    role=\"img\"\u003e\n\u003c/a\u003e\n\n𝒫robabilistic modeling of RNA velocity ⬱\n\n|         |                                                                                                                                                  |\n| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------ |\n| CI/CD   | [![CID][cid-badge]][cid-link] [![codecov][codecov-badge]][codecov-link] [![pre-commit.ci status][precommit-badge]][precommit-link]               |\n| Docs    | [![Cloudflare Pages][cloudflare-badge]][cloudflare-link] [![Preprint][preprint-badge]][preprint-link]                                            |\n| Package | [![PyPI - Version][pypi-badge]][pypi-link] [![Conda-forge badge][conda-forge-badge]][anaconda-link] [![Docker image][docker-badge]][docker-link] |\n| Meta    | [![pyro-ppl-badge]][pyro-ppl-link] [![flyte-badge]][flyte-link] [![hydra-zen-badge]][hydra-zen-link] [![scvi-tools-badge]][scvi-tools-link]      |\n|         | [![bear-badge]][bear-link] [![black-badge]][black-link] [![License][license-badge]][license-link] [![Tuple][tuple-badge]][tuple-link]            |\n\n[bear-badge]: https://raw.githubusercontent.com/beartype/beartype-assets/main/badge/bear-ified.svg\n[bear-link]: https://beartype.readthedocs.io\n[cid-badge]: https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml/badge.svg?branch=main\n[cid-link]: https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml\n[precommit-badge]: https://results.pre-commit.ci/badge/github/pinellolab/pyrovelocity/main.svg\n[precommit-link]: https://results.pre-commit.ci/latest/github/pinellolab/pyrovelocity/main\n[flyte-badge]: https://storage.googleapis.com/pyrovelocity/badges/flyte-carrier.svg\n[flyte-link]: https://docs.flyte.org\n[hydra-zen-badge]: https://storage.googleapis.com/pyrovelocity/badges/Hydra-zen.svg\n[hydra-zen-link]: https://mit-ll-responsible-ai.github.io/hydra-zen/\n[cloudflare-badge]: https://img.shields.io/badge/Docs-pages-gray.svg?style=flat\u0026logo=cloudflare\u0026color=F26722\n[cloudflare-link]: https://docs.pyrovelocity.net\n[preprint-badge]: https://img.shields.io/badge/doi-10.1101/2022.09.12.507691v2-B31B1B\n[preprint-link]: https://doi.org/10.1101/2022.09.12.507691\n[pypi-badge]: https://img.shields.io/pypi/v/pyrovelocity.svg?logo=pypi\u0026label=PyPI\u0026color=F26722\u0026logoColor=F26722\n[pypi-link]: https://pypi.org/project/pyrovelocity/\n[conda-forge-badge]: https://img.shields.io/conda/vn/conda-forge/pyrovelocity.svg?logo=conda-forge\u0026label=conda-forge\u0026color=F26722\n[anaconda-link]: https://anaconda.org/conda-forge/pyrovelocity\n[docker-badge]: https://img.shields.io/badge/docker-image-blue?logo=docker\n[docker-link]: https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity\n[codecov-badge]: https://codecov.io/gh/pinellolab/pyrovelocity/branch/main/graph/badge.svg\n[codecov-link]: https://codecov.io/gh/pinellolab/pyrovelocity\n[black-badge]: https://img.shields.io/badge/code%20style-black-000000.svg\n[black-link]: https://github.com/psf/black\n[license-badge]: https://img.shields.io/badge/license-AGPL%203-gray.svg?color=F26722\n[license-link]: https://spdx.org/licenses/\n[pyro-ppl-badge]: https://storage.googleapis.com/pyrovelocity/badges/Pyro-PPL.svg\n[pyro-ppl-link]: https://pyro.ai\n[scvi-tools-badge]: https://storage.googleapis.com/pyrovelocity/badges/scvi-tools.svg\n[scvi-tools-link]: https://scvi-tools.org\n[tuple-badge]: https://img.shields.io/badge/Tuple%20❤️%20OSS-5A67D8?logo=tuple\n[tuple-link]: https://tuple.app/github-badge\n\n\u003c/div\u003e\n\n---\n\n[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.\nIt provides posterior estimates of gene expression parameters, predictive estimates of gene expression states, and local estimates of cell state transition probabilities.\nIt 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.\n\n---\n\n## Documentation 📒\n\nPlease see the [Documentation](https://docs.pyrovelocity.net).\n\n## Changelog 🔀\n\nChanges for each release are listed in the [Changelog](https://docs.pyrovelocity.net/about/changelog).\n\n## Contributing ✨\n\nPlease review the [Contributing Guide](https://docs.pyrovelocity.net/about/contributing) for instructions on setting up a development environment and submitting pull requests.\n\n## Community 🏘\n\nIf 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).\n\nIf 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\n\n- 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\n- provide a [minimal reproducible example](https://en.wikipedia.org/wiki/Minimal_reproducible_example) of the problem or proposed improvement.\n\nWe are always interested in discussions and issues that can help to improve the [Documentation](https://docs.pyrovelocity.net).\n\n## License ⚖️\n\n[AGPL](https://github.com/pinellolab/pyrovelocity/blob/main/LICENSE)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpinellolab%2Fpyrovelocity","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpinellolab%2Fpyrovelocity","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpinellolab%2Fpyrovelocity/lists"}