scvitools

What problem does it solve?

scvi-tools provides a unified, probabilistic framework for analyzing single-cell omics data, enabling scalable modeling, integration, and interpretation across diverse modalities.

Core Features & Use Cases

• End-to-end single-cell analysis including preprocessing, latent representation, and visualization.
• Multimodal modeling for RNA, protein, and chromatin data (e.g., scVI, totalVI, MultiVI) and integration across batches.
• Differential expression and differential abundance analyses across cell types and conditions.
• Use Case: Integrate PBMC scRNA-seq and CITE-seq data across samples, then identify cell-type-specific markers and trajectories.

Quick Start

1. Install scvi-tools and load an AnnData object.
2. Choose a model (e.g., SCVI) and train to obtain latent embeddings.
3. Use built-in utilities for visualization, DE, and integration tasks.