1. Install Python 3.7. We typically use the Miniconda Python distribution and Linux.

  1. 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.

scVI installation

Install scVI in one of the following ways:

Through conda:

conda install scvi -c bioconda -c conda-forge

Through pip:

pip install scvi

Through pip with packages to run notebooks. This installs scanpy, etc.:

pip install scvi[notebooks]

Nightly version - clone this repo and run:

pip install .

For development - clone this repo and run:

pip install -e .[test,notebooks]

If you wish to use multiple GPUs for hyperparameter tuning, install MongoDb.