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 scvi-tools manuscript as well as the publication describing the model, which can be found in the corresponding documentation.
The user guide provides distilled mathematical descriptions of the models implemented in scvi-tools and connects the math with the code.
The tutorials walk you through real-world applications of scvi-tools models. Developer tutorials help you build new probabilistic models.
Find a bug? Interested in improving scvi-tools? Checkout our GitHub for the latest developments.