jstjohn / scVI-dev

Development branch of the scVI project in PyTorch

scVI

Single-cell Variational Inference

• Free software: MIT license
• Documentation: https://scvi.readthedocs.io.

Installation

1. Install PyTorch: http://pytorch.org
2. Install this repository from source: git clone https://github.com/YosefLab/scVI-dev.git
3. Refer to the examples/ subdirectory for Jupyter notebooks that illustrate usage.

Benchmarks

To recreate the results appearing in the paper referenced below, run

python ./run_benchmarks.py --dataset=cortex

References

Romain Lopez, Jeffrey Regier, Michael B Cole, Michael Jordan, Nir Yosef. "Bayesian Inference for a Generative Model of Transcriptome Profiles from Single-cell RNA Sequencing." In submission. Preprint available at https://www.biorxiv.org/content/early/2018/03/30/292037