scvi-tools

Trains and applies scvi-tools probabilistic deep generative models (scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, Solo, CellAssign, MrVI and others) on AnnData or MuData single-cell data using PyTorch. Covers batch correction, integration, cell type annotation, probabilistic differential expression, and scRNA-seq, ATAC-seq, CITE-seq, spatial and methylation data. Use when integrating batches or datasets with scVI, annotating cells with scANVI, jointly modeling RNA and protein or ATAC, deconvolving spatial spots, or testing differential expression with uncertainty. For standard preprocessing and clustering pipelines, use scanpy instead.

Version

1.2

License

BSD-3-Clause license