scvi-multivi

What problem does it solve?

MultiVI jointly integrates paired and unpaired single-cell RNA and ATAC data using scvi-tools, producing a shared latent embedding with cross-modality imputation. Use when combining 10x Multiome with RNA-only or ATAC-only datasets, when running differential expression plus differential accessibility on joint embeddings, or for multiome batch correction. For ATAC-only analysis use scvi-peakvi; for regulatory TF-to-gene inference on unpaired data use scglue-unpaired-multiomics-integration.

Core Features & Use Cases

• Joint RNA+ATAC integration with cross-modality imputation producing a shared latent representation.
• Supports combining 10x Multiome with RNA-only or ATAC-only datasets and joint differential analyses.
• Provides guidance for data preparation, model configuration, and interpretation of outputs (latent space, imputed modalities).

Quick Start

Prepare an AnnData object with RNA and ATAC modalities and train a scvi-tools MULTIVI model to generate a joint latent embedding and cross-modal imputations.