scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy.
Install / Use
npx skills add K-Dense-AI/scientific-agent-skills --skill scanpyInstalls into whichever agent you are using.
SKILL.md
Installable skill definition
Quality Score
Category
AutomationSupported Platforms
Tags
Our assessment of scanpy
scanpy scores 89/100 on our quality scale, 237th of 1,003 Automation skills we index (top 24%).
We have not analysed the SKILL.md file itself yet, so the content part of this score is an estimate until our crawler reaches it.
With 46,441 GitHub stars, it is one of the more widely adopted skills in the catalogue.
Maintenance, license and trust
- The repository was last updated 3 days ago, so scanpy is actively maintained.
- It is released under the MIT license, a permissive license that allows use, modification and commercial use with attribution.
- Its trust signals score 100/100, with no cautions. These come from repository metadata, not a code audit — read the skill file before letting an agent act on it.
scanpy compared with similar skills
All 4 of these similar skills score higher than scanpy; compare them before choosing.
| Skill | Score | Stars | Updated | Format |
|---|---|---|---|---|
| scanpy (this skill)by K-Dense-AI | 89 | 46.4k | 3d ago | SKILL.md |
| Agent-Reachby Panniantong | 100 | 85.3k | 9d ago | CLAUDE.md |
| rufloby ruvnet | 100 | 73.2k | today | CLAUDE.md |
| Scraplingby D4Vinci | 100 | 83.4k | today | MCP Server |
| algorithmic-artby anthropics | 100 | 177.9k | 2d ago | SKILL.md |
Frequently asked questions
- How do I install scanpy?
- Run
npx skills add K-Dense-AI/scientific-agent-skills --skill scanpy. The install tabs above show the steps for each supported agent. - Which AI agents does scanpy work with?
- It is written for Universal, as a SKILL.md file. Other agents that read the same format can often use it too.
- Is scanpy safe to use?
- It is MIT-licensed and scores 100/100 on trust signals. Skills are instructions an agent will follow, so read the file before installing it and do not approve commands you do not understand.
- Is scanpy still maintained?
- The repository was last updated 3 days ago, so scanpy is actively maintained.
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Languages
Trust signals
From repository metadata: license, adoption, age and documentation. Not a code audit — see the Safety scan above for what the skill file itself contains.