Single-cell Variational Inference
- Free software: MIT license
- Documentation: https://scvi.readthedocs.io.
- Install Python 3.6 or later. We typically use the Miniconda Python distribution.
- Install PyTorch. If you have an Nvidia GPU, be sure to install a version of PyTorch that supports it -- scVI runs much faster with a discrete GPU.
- Install scVI through conda (
conda install scvi -c bioconda) or through pip (
pip install scvi). Alternatively, you may download or clone this repository and run
python setup.py install.
- Follow along with our Jupyter notebooks to quickly get familiar with scVI!
Romain Lopez, Jeffrey Regier, Michael Cole, Michael I. Jordan, Nir Yosef. "Deep generative modeling for single-cell transcriptomics" Nature Methods, in press (accepted Oct 26, 2018). Preprint available at https://www.biorxiv.org/content/early/2018/03/30/292037