https://github.com/theislab/drvi
Unsupervised Deep Disentangled Representation of Single-Cell Omics
https://github.com/theislab/drvi
anndata bioinformatics disentanglement integration python single-cell transcriptomics
Last synced: 4 months ago
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Unsupervised Deep Disentangled Representation of Single-Cell Omics
- Host: GitHub
- URL: https://github.com/theislab/drvi
- Owner: theislab
- License: bsd-3-clause
- Created: 2024-10-24T14:55:16.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-09-29T19:20:14.000Z (4 months ago)
- Last Synced: 2025-09-29T21:29:25.316Z (4 months ago)
- Topics: anndata, bioinformatics, disentanglement, integration, python, single-cell, transcriptomics
- Language: Python
- Homepage: https://drvi.readthedocs.io/
- Size: 14 MB
- Stars: 51
- Watchers: 1
- Forks: 5
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
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README
# DRVI
[![Build][badge-build]][link-build]
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[![Python Version][badge-pyver]][link-pypi]
[badge-build]: https://github.com/theislab/drvi/actions/workflows/build.yaml/badge.svg
[badge-tests]: https://github.com/theislab/drvi/actions/workflows/test.yaml/badge.svg
[link-build]: https://github.com/theislab/drvi/actions/workflows/build.yaml
[link-tests]: https://github.com/theislab/drvi/actions/workflows/test.yaml
[badge-docs]: https://img.shields.io/readthedocs/drvi/latest.svg?label=Read%20the%20Docs
[badge-pyver]: https://img.shields.io/pypi/pyversions/drvi-py
Unsupervised Deep Disentangled Representation of Single-Cell Omics
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [Tutorials][link-tutorials], specially
- [A demo](https://drvi.readthedocs.io/latest/tutorials/external/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.
- [API documentation][link-api], specially
- [DRVI Model](https://drvi.readthedocs.io/latest/api/generated/drvi.model.DRVI.html)
- [DRVI utility functions (tools)](https://drvi.readthedocs.io/latest/api/tools.html)
- [DRVI plotting functions](https://drvi.readthedocs.io/latest/api/plotting.html)
## System requirements
We recommend running DRVI on a recent Linux distribution.
DRVI is actively tested on the latest LTS version of Ubuntu (currently 24.04 LTS).
For optimal performance, we highly recommend using a GPU with CUDA capabilities.
While CPU-based systems are supported, GPU-powered systems are strongly recommended for optimal performance.
## Installation
You need to have Python 3.10, 3.11, or 3.12 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 options to install drvi:
1. Install the latest release of `drvi-py` from [PyPI][link-pypi], which should take around two minutes:
```bash
pip install drvi-py
```
1. Install the latest development version:
```bash
pip install git+https://github.com/theislab/drvi.git@main
```
Please be sure to install a version of [PyTorch][pytorch-home] that is compatible with your GPU.
Dependencies are installed automatically, please take a look at the versions for different dependencies in `pyproject.toml` if needed.
[pytorch-home]: https://pytorch.org/
## Release notes
See the [changelog][changelog].
## Contact
If you found a bug, please use the [issue tracker][issue-tracker].
## Citation
If DRVI is helpful in your research, please consider citing the following paper:
> Moinfar, A. A. & Theis, F. J.
> **Unsupervised deep disentangled representation of single-cell omics.**
> bioRxiv 2024.11.06.622266 (2024) [doi:10.1101/2024.11.06.622266](https://doi.org/10.1101/2024.11.06.622266).
## Reproducibility
Code, notebooks, and instructions to reproduce the results from the paper are available at the [reproducibility repository][repr-repo].
[repr-repo]: https://github.com/theislab/drvi_reproducibility
[issue-tracker]: https://github.com/theislab/drvi/issues
[changelog]: https://drvi.readthedocs.io/latest/changelog.html
[link-docs]: https://drvi.readthedocs.io
[link-api]: https://drvi.readthedocs.io
[link-tutorials]: https://drvi.readthedocs.io/latest/tutorials/index.html
[link-pypi]: https://pypi.org/project/drvi-py