{"id":31805718,"url":"https://github.com/theislab/cellflow","last_synced_at":"2025-10-11T02:57:41.299Z","repository":{"id":279442342,"uuid":"827394164","full_name":"theislab/CellFlow","owner":"theislab","description":"Modeling complex perturbations with CellFlow","archived":false,"fork":false,"pushed_at":"2025-09-29T19:20:12.000Z","size":12913,"stargazers_count":86,"open_issues_count":64,"forks_count":16,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-30T07:27:57.433Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://cellflow.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","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.rst","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":"2024-07-11T15:13:27.000Z","updated_at":"2025-09-30T05:31:10.000Z","dependencies_parsed_at":"2025-04-14T07:30:32.670Z","dependency_job_id":"6847fbc9-7b3d-4452-a3b2-0328168b6d78","html_url":"https://github.com/theislab/CellFlow","commit_stats":null,"previous_names":["theislab/cell_flow_perturbation","theislab/cellflow"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/CellFlow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FCellFlow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FCellFlow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FCellFlow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FCellFlow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/CellFlow/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2FCellFlow/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":[],"created_at":"2025-10-11T02:57:36.859Z","updated_at":"2025-10-11T02:57:41.294Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"docs/_static/images/cellflow_dark.png\" width=\"500\" alt=\"CellFlow\"\u003e\n\n[![PyPI](https://img.shields.io/pypi/v/cellflow-tools.svg)](https://pypi.org/project/cellflow-tools/)\n[![Downloads](https://static.pepy.tech/badge/cellflow-tools)](https://pepy.tech/project/cellflow-tools)\n[![CI](https://img.shields.io/github/actions/workflow/status/theislab/cellflow/test.yaml?branch=main)](https://github.com/theislab/cellflow/actions)\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/theislab/CellFlow/main.svg)](https://results.pre-commit.ci/latest/github/theislab/CellFlow/main)\n[![Codecov](https://codecov.io/gh/theislab/cellflow/branch/main/graph/badge.svg?token=Rgtm5Tsblo)](https://codecov.io/gh/theislab/cellflow)\n[![Docs](https://img.shields.io/readthedocs/cellflow)](https://cellflow.readthedocs.io/en/latest/)\n\nCellFlow - Modeling Complex Perturbations with Flow Matching \n============================================================\n\nCellFlow is a framework for predicting single-cell phenotypes induced by complex perturbations. It is quite flexible and enables researchers to systematically explore how cells respond to a wide range of experimental interventions, including drug treatments, genetic modifications, cytokine stimulation, morphogen pathway modulation or even entire organoid protocols.\n\nCheck out the [preprint](https://www.biorxiv.org/content/10.1101/2025.04.11.648220v1.abstract) for details!\n\n## Example Applications\n\n- Modeling the effect of single and combinatorial drug treatments\n- Predicting the phenotypic response to genetic perturbations\n- Modeling the development of perturbed organisms\n- Cell fate engineering\n- Optimizing protocols for growing organoids\n- ... and more; check out the [documentation](https://cellflow.readthedocs.io) for more information.\n\n\nInstallation\n------------\nInstall **CellFlow** by running::\n\n    pip install cellflow-tools\n\n\nIn order to install **CellFlow** in editable mode, run::\n\n    git clone https://github.com/theislab/cellflow\n    cd cellflow\n    pip install -e .\n\nFor further instructions how to install jax, please refer to https://github.com/google/jax.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fcellflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fcellflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fcellflow/lists"}