scvi-tools (single-cell variational inference tools) [Gayoso21] is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley. scvi-tools has two components

  • Interface for easy use of a range of probabilistic models for single-cell omics (e.g., scVI, scANVI, totalVI).

  • Tools to build new probabilistic models, which are powered by PyTorch, PyTorch Lightning, and Pyro.

If you find a model useful for your research, please consider citing the corresponding publication, which can be found in the corresponding model documentation.

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New to scvi-tools? Check out the installation guide.

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User guide

The tutorials provide in-depth information on running scvi-tools models.

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API reference

The API reference contains a detailed description of the scvi-tools API.

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Developer guide

Want to develop new models with scvi-tools? The developer guide will help you through the process.