{"id":31805731,"url":"https://github.com/theislab/regvelo","last_synced_at":"2025-10-11T02:57:50.338Z","repository":{"id":268870639,"uuid":"602313134","full_name":"theislab/regvelo","owner":"theislab","description":"inferring regulatory cellular dynamics","archived":false,"fork":false,"pushed_at":"2025-09-20T13:10:28.000Z","size":73664,"stargazers_count":56,"open_issues_count":2,"forks_count":5,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-20T14:51:33.695Z","etag":null,"topics":["generative-model","grn-inference","perturbation-analysis","rna-velocity-estimation","single-cell-dynamics"],"latest_commit_sha":null,"homepage":"https://regvelo.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":null,"contributing":null,"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":"2023-02-16T00:04:56.000Z","updated_at":"2025-09-12T10:55:46.000Z","dependencies_parsed_at":"2025-05-07T16:21:06.130Z","dependency_job_id":"aad871fc-f705-4a7d-9983-bc38c01a4874","html_url":"https://github.com/theislab/regvelo","commit_stats":null,"previous_names":["theislab/regvelo"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/regvelo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fregvelo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fregvelo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fregvelo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fregvelo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/regvelo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fregvelo/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":["generative-model","grn-inference","perturbation-analysis","rna-velocity-estimation","single-cell-dynamics"],"created_at":"2025-10-11T02:57:48.107Z","updated_at":"2025-10-11T02:57:50.329Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# RegVelo: gene-regulatory-informed dynamics of single cells\n\n\u003cimg src=\"https://github.com/theislab/regvelo/blob/main/docs/_static/img/overview_fig.png?raw=true\" alt=\"RegVelo\" width=\"600\" /\u003e\n\n**RegVelo** is an end-to-end framework to infer regulatory cellular dynamics through coupled splicing dynamics. \nSee our [RegVelo manuscript](https://www.biorxiv.org/content/10.1101/2024.12.11.627935v1) and [documentation](https://regvelo.readthedocs.io/en/latest/index.html) to learn more. \n\nFeel free to open an [issue](https://github.com/theislab/regvelo/issues/new) if you encounter a bug, need our help or just want to make a comment/suggestion.\n\nRegVelo's key applications\n--------------------------\n- Estimate RNA velocity governed by gene regulation.\n- Infer latent time to indicate the cellular differentiation process.\n- Estimate intrinsic and extrinsic velocity uncertainty [Gayoso et al. (2024)](https://www.nature.com/articles/s41592-023-01994-w).\n- Estimate regulon perturbation effects via CellRank framework ([Lange et al. (2022)](https://www.nature.com/articles/s41592-021-01346-6), [Weiler et al. (2024)](https://www.nature.com/articles/s41592-024-02303-9)).\n\n\n## Getting started\n\nWe have [tutorials](https://regvelo.readthedocs.io/en/latest/tutorials/index.html) to help you get started.\n\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system.\n\nThere are several options to intall regvelo:\n\n1. Install the latest release of `regvelo` from PyPI via\n\n```bash\n  pip install regvelo\n```\n\n2. Install the latest development version via\n\n```bash\n  pip install git+https://github.com/theislab/regvelo.git@main\n```\n\n## Citation\n\nIf you find RegVelo useful for your research, please consider citing our work as:\n\n```\n  @article{wang2024regvelo,\n    title={RegVelo: gene-regulatory-informed dynamics of single cells},\n    author={Wang, Weixu and Hu, Zhiyuan and Weiler, Philipp and Mayes, Sarah and Lange, Marius and Wang, Jingye and Xue, Zhengyuan and Sauka-Spengler, Tatjana and Theis, Fabian J},\n    journal={bioRxiv},\n    pages={2024--12},\n    year={2024},\n    publisher={Cold Spring Harbor Laboratory}\n  }\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fregvelo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fregvelo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fregvelo/lists"}