About
Scanpy is a Python toolkit for analyzing single-cell RNA-seq data, built on the AnnData object for managing expression matrices and metadata. It enables key analyses like clustering, dimensionality reduction (PCA/UMAP), and trajectory inference to identify cell types and states. Use it to process high-dimensional gene expression data for visualizing cell populations and discovering rare cell types.
Quick Install
Claude Code
Recommendednpx skills add tondevrel/scientific-agent-skills -a claude-code/plugin add https://github.com/tondevrel/scientific-agent-skillsgit clone https://github.com/tondevrel/scientific-agent-skills.git ~/.claude/skills/scanpyCopy and paste this command in Claude Code to install this skill
GitHub Repository
Frequently asked questions
What is the scanpy skill?
scanpy is a Claude Skill by tondevrel. Skills package instructions and resources that Claude loads on demand, so Claude can perform scanpy-related tasks without extra prompting.
How do I install scanpy?
Use the install commands on this page: add scanpy to Claude Code as a plugin, or clone its repository into your skills directory, then restart Claude so it picks up the skill.
What category does scanpy belong to?
scanpy is in the Design category, tagged design and data.
Is scanpy free to use?
Yes. scanpy is listed on AIMCP and free to install. It runs inside Claude, so no separate service account is required to use the skill itself.
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