scvi-tools

scvi-tools is a Data skill for Claude Code, published by anthropics in knowledge-work-plugins.

23.3K stars2.8K forkson anthropics/knowledge-work-pluginsAdded 2026/07/19Repository updated 2026/08/06

Install in seconds

Install scvi-tools

Copy scvi-tools into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/scvi-tools ~/.claude/skills/scvi-tools

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/anthropics/knowledge-work-plugins.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: bio-research/skills/scvi-tools/SKILL.md in anthropics/knowledge-work-plugins
Installs to: ~/.claude/skills/scvi-tools
Collection: One of 26 skills cataloged from this repository
Category: Data — 812 skills

What scvi-tools does

Provides deep learning-based single-cell analysis workflows using scvi-tools for data integration, batch correction, multi-modal analysis, spatial transcriptomics, and RNA velocity.

scvi-tools is cataloged under Data on DirSkills.

Documentation

README

Excerpt

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

This is the opening of the README. Read the full README on GitHub.

Frequently asked about scvi-tools

What else does anthropics publish alongside scvi-tools?
scvi-tools is one of 26 skills that DirSkills catalogs from anthropics/knowledge-work-plugins, the repository it ships in. Its siblings there include Accessibility Review, Analyze Data and Bio-Research Start. Each one is a separate skill with its own page in this directory, installs the same way scvi-tools does, and is maintained by anthropics in that same repository. The rest of the collection is listed on the anthropics/knowledge-work-plugins page.
How does scvi-tools compare to other Data skills?
scvi-tools ranks #90 by stars among the 812 Data skills in this catalog. The most-starred ones next to it are Benchmark Methodology, Jupyter Notebook and Solana. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of scvi-tools against them. Open each page to compare what they document and how they install.