Unsupervised Deep Disentangled Representation of Single-Cell Omics
Please refer to the documentation. In particular, the
- Tutorials, specially
- A demo of how to train DRVI and interpret the latent dimensions.
- API documentation, specially
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.
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.
There are several options to install drvi:
- Install the latest release of
drvi-pyfrom PyPI, which should take around two minutes:
pip install drvi-py- Install the latest development version:
pip install git+https://github.com/theislab/drvi.git@mainPlease be sure to install a version of PyTorch 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.
See the changelog.
If you found a bug, please use the issue tracker.
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.
Code, notebooks, and instructions to reproduce the results from the paper are available at the reproducibility repository.