scvi-tools

scvi-tools is a comprehensive Python framework designed for probabilistic modeling of single-cell genomics data. Built on PyTorch and PyTorch Lightning, it provides researchers with robust deep generative models to perform essential tasks like dimensionality reduction, batch correction, and differential expression across diverse modalities including scRNA-seq, scATAC-seq, and spatial transcriptomics. This skill streamlines the entire analytical pipeline—from data registration and model training to latent representation extraction—ensuring seamless integration with the wider Scanpy ecosystem for advanced biological discovery.

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