scvi-tools

Q: What is a Claude Code skill and how does the scvi-tools skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. scvi-tools is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Content category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Content · Sub-category: content-misc · Last updated: 2026-08-02

type:integration

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.

Security AStatic scan found no risk patternsHow grading works ›

From the source SKILL.md

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

What this skill does

scvi-tools is a community-contributed Claude Code skill in the content-misc sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/scvi-tools-yongjianwan-agentskill/ and loads when your prompt matches the skill's trigger.

Who uses this skill

The scvi-tools Claude Code skill is built for content creators, marketers, copywriters, SEO professionals, and editorial teams. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 174,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/scvi-tools-yongjianwan-agentskill
curl -L https://claudskills.com/skills/scvi-tools-yongjianwan-agentskill/SKILL.md \
  -o ~/.claude/skills/scvi-tools-yongjianwan-agentskill/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/scvi-tools-yongjianwan-agentskill/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/scvi-tools-yongjianwan-agentskill/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\scvi-tools-yongjianwan-agentskill\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the scvi-tools Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/scvi-tools-yongjianwan-agentskill/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the scvi-tools skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the scvi-tools skill?

Use scvi-tools when your Claude Code task falls under the Content category — specifically in the content misc area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use scvi-tools" or describe the task and let Claude pick). Browse related skills at /category/content/.

What is a Claude Code skill and how does the scvi-tools skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. scvi-tools is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Content category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/ai-ml/scvi-tools-yongjianwan-agentskill/SKILL.md
License: MIT
Author: majiayu000
Website: https://majiayu000.github.io/claude-skill-registry/

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

majiayu000. (2026). scvi-tools [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/scvi-tools-yongjianwan-agentskill/

BibTeX

@misc{scvi-tools-yongjianwan-agentskill-2026,
  author    = {majiayu000},
  title     = {scvi-tools [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/scvi-tools-yongjianwan-agentskill/}
}

Embed this skill

Promote, attribute, or link this skill from your own README, blog post, or documentation. All three snippets are free to use — no sign-up, no API key. More distribution surfaces →

Badge

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Security scan

Grade A · scanned 2026-08-02 — free static scan against the OWASP Agentic Skills Top 10.

No risk patterns were found in any of the ten OWASP-aligned categories. How grading works ›

✓ Prompt injection
✓ Data exfiltration
✓ Supply chain
✓ Reverse shell
✓ Credentials
✓ Execution
✓ Filesystem
✓ Persistence
✓ Obfuscation
✓ Network

Show this grade on your repo (click to copy):

[![Security: A](https://img.shields.io/badge/Security-A-2e7d32)](https://claudskills.com/skills/scvi-tools-yongjianwan-agentskill/#security)