---
title: "scvi-tools Deep Learning Skill"
type: skill
id: "knowledge-work-plugins/bio-research/scvi-tools"
category: "Research"
publisher: "Anthropic"
license: "Apache-2.0"
source: "https://github.com/anthropics/knowledge-work-plugins/tree/d900840"
canonical: "https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scvi-tools"
open_in_pho: "https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Fscvi-tools&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library"
---

# scvi-tools Deep Learning Skill

Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.

Source: Anthropic (Apache 2.0), copied at a pinned commit. Free to use. Part of the Phở Skills library (https://labs.pho.chat/en/skills).
Skill set: Bio research (https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research.md).

## What it covers
- How to Use This Skill
- When to Use This Skill
- Model Selection Guide
- Workflow Reference Files
- CLI Scripts
  - Pipeline Scripts
  - Example Workflow
  - Python Utilities
- Critical Requirements
- Quick Decision Tree
- Key Resources

## Other skills in this set
- [Instrument Data to Allotrope Converter](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/instrument-data-to-allotrope.md): Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data…
- [nf-core Pipeline Deployment](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/nextflow-development.md): Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers…
- [Scientific Problem Selection Skills](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/scientific-problem-selection.md): This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users…
- [Single-Cell RNA-seq Quality Control](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/single-cell-rna-qc.md): Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis…
- [Bio-Research Start](https://labs.pho.chat/en/skills/knowledge-work-plugins/bio-research/start.md): Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are…

## Use it
- In Phở: open https://pho.chat/customize?item=knowledge-work-plugins%2Fbio-research%2Fscvi-tools&utm_source=labs&utm_medium=skill-page&utm_campaign=skills-library and press Try, or add it so Phở loads it whenever a request matches. Phở works with your own API key (OpenAI, Anthropic, Google and others).
- Full instructions (original SKILL.md, unchanged): https://labs.pho.chat/skills/raw/knowledge-work-plugins/bio-research/skills/scvi-tools/SKILL.md
- Original files: https://github.com/anthropics/knowledge-work-plugins/tree/d900840 (Apache 2.0).
- Full machine-readable index: https://labs.pho.chat/skills.json