{"id":31805720,"url":"https://github.com/theislab/geome","last_synced_at":"2025-10-11T02:57:41.718Z","repository":{"id":78600988,"uuid":"527641675","full_name":"theislab/geome","owner":"theislab","description":null,"archived":false,"fork":false,"pushed_at":"2025-08-06T12:18:10.000Z","size":21353,"stargazers_count":15,"open_issues_count":9,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-25T12:17:44.521Z","etag":null,"topics":["anndata","graph-learning","microscopy","pytorch-geometric"],"latest_commit_sha":null,"homepage":"https://geome.readthedocs.io/en/latest/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","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}},"created_at":"2022-08-22T16:18:09.000Z","updated_at":"2025-08-06T12:18:15.000Z","dependencies_parsed_at":"2024-06-04T13:03:34.919Z","dependency_job_id":null,"html_url":"https://github.com/theislab/geome","commit_stats":null,"previous_names":["theislab/geome"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/geome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgeome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgeome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgeome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgeome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/geome/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgeome/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","graph-learning","microscopy","pytorch-geometric"],"created_at":"2025-10-11T02:57:38.991Z","updated_at":"2025-10-11T02:57:41.705Z","avatar_url":"https://github.com/theislab.png","language":"Python","readme":"# geome\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/geome/build.yaml?branch=main\n[link-tests]: https://github.com/theislab/geome/actions/workflows/build.yaml\n[badge-docs]: https://img.shields.io/readthedocs/geome\n\nThe repo provides a set of tools for creating PyTorch Geometric (PyG) data objects from AnnData objects, which are commonly used for storing and manipulating single-cell genomics data. In addition, the repo includes functionality for creating PyTorch Lightning (PyTorch-Lightning) DataModule objects from the PyG data objects, which can be used to create graph neural network (GNN) data pipelines. The PyG data objects represent graphs, where the nodes represent cells and the edges represent relationships between the cells, and can be used to perform GNN tasks such as node classification, graph classification, and link prediction. The repo is written in Python and utilizes the PyTorch, PyTorch Geometric, and PyTorch-Lightning libraries.\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n-   [API documentation][link-api].\n\n## Installation\n\nYou need to have Python 3.9 or newer installed on your system. If you don't have\nPython installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).\n\nThere are several alternative options to install geome:\n\n\u003c!--\n1) Install the latest release of `geome` from `PyPI \u003chttps://pypi.org/project/geome/\u003e`_:\n\n```bash\npip install geome\n```\n--\u003e\n\n1. Install the latest development version:\n\n\nWithout GPU support:\n\n```bash\nmamba create -n geome  python=3.10\nmamba activate geome\npip install torch==2.1.0\npip install torch-scatter torch-sparse torch-cluster\npip install git+https://github.com/theislab/geome.git@main\n```\n\nWith GPU:\n\n```bash\nmamba create -n geome  python=3.10\nmamba activate geome\nmamba install pytorch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 pytorch-cuda=12.1 -c pytorch -c nvidia\npip install torch-scatter torch-sparse torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu121.html\npip install git+https://github.com/theislab/geome.git@main\n```\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][scverse-discourse].\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Credits\n\nSome of the data for `DatasetHartmann` is distributed in this package.\nIt was originally retrieved from: https://zenodo.org/record/3951613#.Y9flQS-B1qv\n\nThis project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter] template.\n\n[@cjolowicz]: https://github.com/cjolowicz\n[pypi]: https://pypi.org/\n[hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python\n[file an issue]: https://github.com/theislab/geome/issues\n[pip]: https://pip.pypa.io/\n\n## Citation\n\n\u003e t.b.a\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/theislab/geome/issues\n[changelog]: https://geome.readthedocs.io/changelog.html\n[link-docs]: https://geome.readthedocs.io/\n[link-api]: https://geome.readthedocs.io/en/latest/api.html\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fgeome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fgeome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fgeome/lists"}