Deep Generative Model Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

scmidas

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

scvi

Deep probabilistic analysis of single-cell and spatial omics data

causalegm

CausalEGM: an encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies

scvega

VEGA: a VAE Enhanced by Gene Annotations for interpretable scRNA-seq deep learning

pyroundtrip

Roundtrip: density estimation with deep generative neural networks