single-cell-multi-omics-analysis-scvi

What problem does it solve?

scvi-tools provides probabilistic models for integrated single-cell multi-omics data, enabling robust joint analysis of RNA, chromatin accessibility, and protein measurements while simplifying batch correction and data integration.

Core Features & Use Cases

• Supports single-cell RNA-seq, ATAC-seq, and multimodal data (CITE-seq, multi-omics) with unified APIs for setup, training, and extraction.
• Enables end-to-end workflows for batch correction, data integration across experiments, and cell-type annotation in multi-modal datasets.
• Supports spatial transcriptomics analysis and specialized modalities via structured model families like scVI, scANVI, totalVI, and MultiVI.

Quick Start

Load your AnnData object with raw counts and follow the standard scvi-tools workflow to obtain a batch-corrected latent representation.