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