Scvi Tools

---
name: scvi-tools
description: Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
license: BSD-3-Clause license
metadata: {"version": "1.1", "skill-author": "K-Dense Inc."}
---

# scvi-tools

## Overview

scvi-tools is a comprehensive Python framework for probabilistic models in single-cell genomics. Built on PyTorch and PyTorch Lightning, it provides deep generative models using variational inference for analyzing diverse single-cell data modalities. Current stable release: **scvi-tools 1.4.3** (May 2026).

**Model namespaces matter:** core models (scVI, scANVI, totalVI, MultiVI, PeakVI, AUTOZI, CondSCVI, DestVI, LinearSCVI, AmortizedLDA, JaxSCVI) live under `scvi.model`. Most other models (VeloVI, contrastiveVI, CellAssign, PoissonVI, scBasset, MrVI, MethylVI/MethylANVI, CytoVI, SysVI, Decipher, gimVI, scVIVA, ResolVI, Stereoscope, Solo, totalANVI, DIAGVI) live under `scvi.external`. The reference files specify the correct namespace per model.

## When to Use This Skill

Use this skill when:
- Analyzing single-cell RNA-seq data (dimensionality reduction, batch correction, integration)
- Working with single-cell ATAC-seq or chromatin accessibility data
- Integrating multimodal data (CITE-seq, multiome, paired/unpaired datasets)
- Analyzing spatial transcriptomics data (deconvolution, spatial mapping)
- Performing differential expression analysis on single-cell data
- Conducting cell type annotation or transfer learning tasks
- Working with specialized single-cell modalities (methylation, cytometry, RNA velocity)… load the full skill through Skill Me