{"id":31805725,"url":"https://github.com/theislab/drvi","last_synced_at":"2026-03-02T17:16:22.550Z","repository":{"id":261642643,"uuid":"877971131","full_name":"theislab/DRVI","owner":"theislab","description":"Unsupervised Deep Disentangled Representation of Single-Cell Omics","archived":false,"fork":false,"pushed_at":"2025-09-29T19:20:14.000Z","size":14684,"stargazers_count":51,"open_issues_count":7,"forks_count":5,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-29T21:29:25.316Z","etag":null,"topics":["anndata","bioinformatics","disentanglement","integration","python","single-cell","transcriptomics"],"latest_commit_sha":null,"homepage":"https://drvi.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"docs/contributing.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-10-24T14:55:16.000Z","updated_at":"2025-09-23T19:46:03.000Z","dependencies_parsed_at":"2025-01-27T22:25:43.028Z","dependency_job_id":"b674bf0c-229b-4ab9-92db-a263aaa28365","html_url":"https://github.com/theislab/DRVI","commit_stats":null,"previous_names":["theislab/drvi"],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/DRVI","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FDRVI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FDRVI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FDRVI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FDRVI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/DRVI/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FDRVI/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005953,"owners_count":26084009,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["anndata","bioinformatics","disentanglement","integration","python","single-cell","transcriptomics"],"created_at":"2025-10-11T02:57:42.532Z","updated_at":"2026-03-02T17:16:22.532Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DRVI\n\n[![Build][badge-build]][link-build]\n[![Tests][badge-tests]][link-tests]\n[![Codecov][badge-codecov]][link-codecov]\n[![Documentation][badge-docs]][documentation]\n[![Python Version][badge-pyver]][pypi]\n[![PyPI Downloads][badge-pypi-downloads]][link-pepy]\n\n[badge-build]: https://github.com/theislab/drvi/actions/workflows/build.yaml/badge.svg\n[badge-tests]: https://github.com/theislab/drvi/actions/workflows/test.yaml/badge.svg\n[badge-codecov]: https://codecov.io/gh/theislab/drvi/graph/badge.svg?token=zeA0Sr3NVF\n[badge-docs]: https://img.shields.io/readthedocs/drvi/latest.svg?label=Read%20the%20Docs\n[badge-pyver]: https://img.shields.io/pypi/pyversions/drvi-py\n[badge-pypi-downloads]: https://static.pepy.tech/personalized-badge/drvi-py?period=total\u0026units=INTERNATIONAL_SYSTEM\u0026left_color=BLACK\u0026right_color=GREEN\u0026left_text=%F0%9F%93%A6+downloads\n\nUnsupervised Deep Disentangled Representation of Single-Cell Omics\n\n\u003ch1 align=\"center\"\u003e\n    \u003cpicture\u003e\n        \u003csource srcset=\"https://raw.githubusercontent.com/theislab/DRVI/main/.github/misc/concept.svg\"\u003e\n        \u003cimg width=\"800\" src=\"https://raw.githubusercontent.com/theislab/DRVI/main/.github/misc/concept.svg\" alt=\"DRVI concept\"\u003e\n    \u003c/picture\u003e\n\u003c/h1\u003e\n\n## Getting started\n\nPlease refer to the [documentation][]. In particular, the\n\n- [Tutorials][], specially\n    - [A demo](https://drvi.readthedocs.io/latest/tutorials/external/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.\n- [API documentation][], specially\n    - [DRVI Model](https://drvi.readthedocs.io/latest/api/generated/drvi.model.DRVI.html)\n    - [DRVI utility functions (tools)](https://drvi.readthedocs.io/latest/api/tools.html)\n    - [DRVI plotting functions](https://drvi.readthedocs.io/latest/api/plotting.html)\n\n## System requirements\n\nWe recommend running DRVI on a recent Linux distribution.\nDRVI is actively tested on the latest LTS version of Ubuntu (currently 24.04 LTS).\n\n\u003c!-- TODO: remove ubuntu version later --\u003e\n\nFor optimal performance, we highly recommend using a GPU with CUDA capabilities.\nWhile CPU-based systems are supported, GPU-powered systems are strongly recommended for optimal performance.\n\n## Installation\n\nYou need to have Python (versions 3.10 to 3.14 supported) installed on your system. If you don't have\nPython installed, we recommend installing [uv][].\n\nThere are several alternative options to install drvi:\n\n\u003c!-- TODO: remove install time! --\u003e\n\n1. Install the latest release of `drvi-py` from [PyPI][], which should take around two minutes:\n\n```bash\npip install drvi-py\n```\n\n1. Install the latest development version:\n\n```bash\npip install git+https://github.com/theislab/drvi.git@main\n```\n\nPlease be sure to install a version of [PyTorch][pytorch-home] that is compatible with your GPU.\nDependencies are installed automatically, please take a look at the versions for different dependencies in `pyproject.toml` if needed.\n\n[pytorch-home]: https://pytorch.org/\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Contact\n\nFor questions and help requests, you can reach out in the [scverse discourse][].\nIf you found a bug, please use the [issue tracker][].\n\n## Citation\n\nIf DRVI is helpful in your research, please consider citing the following paper:\n\n\u003e Moinfar, A. A. \u0026 Theis, F. J.\n\u003e **Disentangling cellular heterogeneity into interpretable biological factors through structured latent representations.**\n\u003e bioRxiv 2024.11.06.622266 (2024) [doi:10.1101/2024.11.06.622266](https://doi.org/10.1101/2024.11.06.622266).\n\n## Reproducibility\n\nCode, notebooks, and instructions to reproduce the results from the paper are available at the [reproducibility repository][].\n\n[link-build]: https://github.com/theislab/drvi/actions/workflows/build.yaml\n[link-tests]: https://github.com/theislab/drvi/actions/workflows/test.yaml\n[link-codecov]: https://codecov.io/gh/theislab/drvi\n[link-pepy]: https://pepy.tech/projects/drvi-py\n\n[uv]: https://github.com/astral-sh/uv\n[scverse discourse]: https://discourse.scverse.org/\n[issue tracker]: https://github.com/theislab/drvi/issues\n[documentation]: https://drvi.readthedocs.io\n[changelog]: https://drvi.readthedocs.io/latest/changelog.html\n[api documentation]: https://drvi.readthedocs.io\n[pypi]: https://pypi.org/project/drvi-py\n[tutorials]: https://drvi.readthedocs.io/latest/tutorials/index.html\n[reproducibility repository]: https://github.com/theislab/drvi_reproducibility\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fdrvi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fdrvi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fdrvi/lists"}