https://github.com/theislab/multigrate
Multigrate: multiomic data integration for single-cell genomics
https://github.com/theislab/multigrate
Last synced: 10 months ago
JSON representation
Multigrate: multiomic data integration for single-cell genomics
- Host: GitHub
- URL: https://github.com/theislab/multigrate
- Owner: theislab
- License: bsd-3-clause
- Created: 2022-04-05T09:19:49.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-10-06T20:18:14.000Z (10 months ago)
- Last Synced: 2025-10-06T22:18:38.989Z (10 months ago)
- Language: Python
- Homepage: https://multigrate.readthedocs.io/en/latest/
- Size: 14.3 MB
- Stars: 27
- Watchers: 0
- Forks: 8
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
- awesome-computational-biology - Multigrate - omics variational autoencoder for integrating single-cell data across RNA, ATAC, and protein modalities with missing-modality support. (Machine Learning Tasks and Models / Foundation Models)
README
# Multigrate: multiomic data integration for single-cell genomics
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/multigrate/test.yaml?branch=main
[link-tests]: https://github.com/theislab/multigrate/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/multigrate
[badge-colab]: https://colab.research.google.com/assets/colab-badge.svg
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api]
and the tutorials:
- [Paired integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/paired_integration_cite-seq.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/paired_integration_cite-seq.ipynb)
- [Trimodal integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/trimodal_integration.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/trimodal_integration.ipynb)
## Installation
You need to have Python 3.10 or newer installed on your system. We recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
To create and activate a new environment:
```bash
mamba create --name multigrate python=3.10
mamba activate multigrate
```
Next, there are several alternative options to install multigrate:
1. Install the latest release of `multigrate` from [PyPI][link-pypi]:
```bash
pip install multigrate
```
2. Or install the latest development version:
```bash
pip install git+https://github.com/theislab/multigrate.git@main
```
## Release notes
See the [changelog][changelog].
## Contact
If you found a bug, please use the [issue tracker][issue-tracker].
## Citation
> Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, and Fabian Theis. 2022. "Integration and querying of multimodal single-cell data with PoE-VAE." _bioRxiv_. https://doi.org/10.1101/2022.03.16.484643.
## Reproducibility
Code and notebooks to reproduce the results from the paper are available at https://github.com/theislab/multigrate_reproducibility.
[issue-tracker]: https://github.com/theislab/multigrate/issues
[changelog]: https://multigrate.readthedocs.io/latest/changelog.html
[link-docs]: https://multigrate.readthedocs.io
[link-api]: https://multigrate.readthedocs.io/latest/api.html
[link-pypi]: https://pypi.org/project/multigrate