ClaudSkills / Science & Research / biology-medicine

Tooluniverse Single Cell

Q: What is a Claude Code skill and how does the Tooluniverse Single Cell 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. Tooluniverse Single Cell is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Science & Research · Sub-category: biology-medicine · Last updated: 2026-06-02

Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering, differential expression (Wilcoxon, t-test, DESeq2), cell type annotation, per-cell-type statistical analysis, gene-expression correlation, batch correction (Harmony), trajectory inference, and cell-cell communication analysis. NEW: Analyzes ligand-receptor interactions between cell types using OmniPath (CellPhoneDB, CellChatDB), scores communication strength, identifies signaling cascades, and handles multi-subunit receptor complexes. Integrates with ToolUniverse gene annotation tools (HPA, Ensembl, MyGene, UniProt) and enrichment tools (gseapy, PANTHER, STRING). Supports h5ad, 10X, CSV/TSV count matrices, and pre-annotated datasets.

From the source SKILL.md

Comprehensive single-cell RNA-seq analysis and expression matrix processing using scanpy, anndata, scipy, and ToolUniverse. Designed for both full scRNA-seq workflows (raw counts to annotated cell types) and targeted expression-level analyses (per-cell-type DE, correlation, ANOVA, clustering).

What this skill does

Tooluniverse Single Cell is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/tooluniverse-single-cell/ and loads when your prompt matches the skill's trigger.

Who uses this skill

The Tooluniverse Single Cell Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ 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/tooluniverse-single-cell
curl -L https://claudskills.com/skills/tooluniverse-single-cell/SKILL.md \
  -o ~/.claude/skills/tooluniverse-single-cell/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/tooluniverse-single-cell/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/tooluniverse-single-cell/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\tooluniverse-single-cell\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 Tooluniverse Single Cell Claude Code skill?

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

What does the Tooluniverse Single Cell 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 Tooluniverse Single Cell skill?

Use Tooluniverse Single Cell when your Claude Code task falls under the Science & Research category — specifically in the biology medicine 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 Tooluniverse Single Cell" or describe the task and let Claude pick). Browse related skills at /category/science/.

What is a Claude Code skill and how does the Tooluniverse Single Cell 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. Tooluniverse Single Cell is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/bg-szy/TOP-SKILLS/blob/HEAD/skills/awesome-skills/tooluniverse-single-cell/SKILL.md
Author: bg-szy
Website: https://bg-szy.github.io/TOP-SKILLS/

Cite this skill

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

APA

bg-szy. (2026). Tooluniverse Single Cell [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/tooluniverse-single-cell/

BibTeX

@misc{tooluniverse-single-cell-2026,
  author    = {bg-szy},
  title     = {Tooluniverse Single Cell [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/tooluniverse-single-cell/}
}

Embed this skill

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Badge

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