scvi-tools (single-cell variational inference tools) 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.
New to scvi-tools? Check out the installation guide.
To the installation guide
The tutorials provide in-depth information on running scvi-tools models.
To the user guide
The API reference contains a detailed description of
the scvi-tools API.
To the API reference
Want to develop new models with scvi-tools? The developer guide
will help you through the process.
To the developer guide