Scvi Tools

scvi-tools Deep Learning Skill

This skill provides guidance for deep learning-based single-cell analysis using scvi-tools, the leading framework for probabilistic models in single-cell genomics.

How to Use This Skill

1. Identify the appropriate workflow from the model/workflow tables below
2. Read the corresponding reference file for detailed steps and code
3. Use scripts in scripts/ to avoid rewriting common code
4. For installation or GPU issues, consult references/environment_setup.md
5. For debugging, consult references/troubleshooting.md

When to Use This Skill

• When scvi-tools, scVI, scANVI, or related models are mentioned
• When deep learning-based batch correction or integration is needed
• When working with multi-modal data (CITE-seq, multiome)
• When reference mapping or label transfer is required
• When analyzing ATAC-seq or spatial transcriptomics data
• When learning latent representations of single-cell data

Model Selection Guide