https://github.com/theislab/geome
https://github.com/theislab/geome
anndata graph-learning microscopy pytorch-geometric
Last synced: 7 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/theislab/geome
- Owner: theislab
- License: mit
- Created: 2022-08-22T16:18:09.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-08-06T12:18:10.000Z (9 months ago)
- Last Synced: 2025-09-25T12:17:44.521Z (7 months ago)
- Topics: anndata, graph-learning, microscopy, pytorch-geometric
- Language: Python
- Homepage: https://geome.readthedocs.io/en/latest/
- Size: 20.4 MB
- Stars: 15
- Watchers: 2
- Forks: 4
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# geome
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/geome/build.yaml?branch=main
[link-tests]: https://github.com/theislab/geome/actions/workflows/build.yaml
[badge-docs]: https://img.shields.io/readthedocs/geome
The 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.
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api].
## Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install geome:
1. Install the latest development version:
Without GPU support:
```bash
mamba create -n geome python=3.10
mamba activate geome
pip install torch==2.1.0
pip install torch-scatter torch-sparse torch-cluster
pip install git+https://github.com/theislab/geome.git@main
```
With GPU:
```bash
mamba create -n geome python=3.10
mamba activate geome
mamba install pytorch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 pytorch-cuda=12.1 -c pytorch -c nvidia
pip install torch-scatter torch-sparse torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu121.html
pip install git+https://github.com/theislab/geome.git@main
```
## Release notes
See the [changelog][changelog].
## Contact
For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].
## Credits
Some of the data for `DatasetHartmann` is distributed in this package.
It was originally retrieved from: https://zenodo.org/record/3951613#.Y9flQS-B1qv
This project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter] template.
[@cjolowicz]: https://github.com/cjolowicz
[pypi]: https://pypi.org/
[hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python
[file an issue]: https://github.com/theislab/geome/issues
[pip]: https://pip.pypa.io/
## Citation
> t.b.a
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/theislab/geome/issues
[changelog]: https://geome.readthedocs.io/changelog.html
[link-docs]: https://geome.readthedocs.io/
[link-api]: https://geome.readthedocs.io/en/latest/api.html