Deep learning for single-cell analysis using scvi-tools. This skill.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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
| Data Type | Model | Primary Use Case |
|-----------|-------|------------------|
| scRNA-seq | **scVI** | Unsupervised integration, DE, imputation |
…
The line at the top of this page pins the label git:20260902.9fe0199, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
GET https://markdownregistry.com/api/v1/artifacts/art_crclvxumu46mqk3a
GET https://markdownregistry.com/api/v1/resolve?ref=nota-america/forgecat-agent-profiles/scvi-tools
GET https://markdownregistry.com/api/v1/blob/0772fba63888abfa9225c2277aa4f20e0aa57fb0811a9d910ff93337a338dedc
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/api-and-interface-design/SKILL.md · Guides stable API and interface design. Use when designing APIs,
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/browser-testing-with-devtools/SKILL.md · Tests in real browsers via Chrome DevTools MCP. Use when building
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nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/code-review-and-quality/SKILL.md · Conducts multi-axis code review. Use before merging any change. Use
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/code-simplification/SKILL.md · Simplifies code for clarity. Use when refactoring code for clarity
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/constraint-driven-development/SKILL.md · Establishes a project's quality bar as a written contract and stops
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/context-engineering/SKILL.md · Optimizes agent context setup. Use when starting a new session,
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/deprecation-and-migration/SKILL.md · Manages deprecation and migration. Use when removing old systems,
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/documentation-and-adrs/SKILL.md · Records decisions and documentation. Use when you need to document
nota-america/forgecat-agent-profiles · profiles/addyosmani/agent-skills/for-claude/.claude/skills/doubt-driven-development/SKILL.md · Subjects every non-trivial decision to a fresh-context adversarial
aipoch/open-science · resources/skills/scvi-tools/SKILL.md · Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised…
nota-america/forgecat-agent-profiles · profiles/anthropics/knowledge-work-plugins/anthropics_knowledge-work-plugins_bio-research/for-codex/.agents/skills/scvi-tools/SKILL.md · Deep learning for single-cell analysis using scvi-tools. This skill
yichen-zju/claude-for-research · claude/skills/scvi-tools/SKILL.md · Run scvi-tools single-cell workflows. Use when a task asks for scVI/scANVI setup, latent embeddings, batch correction…
pengqianhan/ai-human-research-os · research-skills-hub/claude-science-skills/skills/scvi-tools/SKILL.md · Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised…
