A computational-biology plugin for work involving single-cell data, spatial omics, multi-omics, databases, and scientific workflows. Omics means large-scale measurements of biological molecules such as genes or proteins.

Use it for computational-biology workflows and retrospectives involving single-cell, spatial, or multi-omics data.

It brings related biology workflows together for projects that combine experimental data, databases, and analysis methods.

compbio — Plugin for Claude Code by CHENyiru3/AI-Skills-Collections

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo

git clone --depth 1 https://github.com/CHENyiru3/AI-Skills-Collections

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/plugins/chenyiru3/ai-skills-collections/compbio/github.svg)](https://agentmods.dev/plugins/chenyiru3/ai-skills-collections/compbio)

Your own site

<a href="https://agentmods.dev/plugins/chenyiru3/ai-skills-collections/compbio"><img src="https://agentmods.dev/badge/plugins/chenyiru3/ai-skills-collections/compbio/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/plugins/chenyiru3/ai-skills-collections/compbio"><img src="https://agentmods.dev/badge/plugins/chenyiru3/ai-skills-collections/compbio.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session not measured What this adds to a session before it is invoked.

When invoked not measured The manifest loads nothing itself; its 38 skills cost 1,681 tokens a session between them.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

compbio scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude-plugin/marketplace.json#compbio · 46 lines

What it actually says

{
  "name": "compbio",
  "description": "Computational biology — perturbation analysis, single-cell, spatial omics, databases, project continuity",
  "source": "./skills-market/compbio",
  "strict": false,
  "skills": [
    "./databases/ensembl",
    "./databases/geo",
    "./databases/human-cell-atlas",
    "./databases/kegg",
    "./databases/reactome",
    "./expert-workflows/computational-biology-project-manager",
    "./expert-workflows/computational-biology-retrospective",
    "./expert-workflows/critique-bio-manuscript",
    "./expert-workflows/draft-spatial-methods",
    "./expert-workflows/explain-bio-dl-model",
    "./multiomics/integration-tools/scribble",
    "./multiomics/metabolomics/metabolomics-workbench",
    "./multiomics/proteomics/uniprot",
    "./multiomics/scATAC-seq/archr",
    "./multiomics/scATAC-seq/signac",
    "./multiomics/scRNA-seq/pydeseq2",
    "./single-cell/analysis/anndata",
    "./single-cell/analysis/anndatar",
    "./single-cell/analysis/monocle3",
    "./single-cell/analysis/pertpy",
    "./single-cell/analysis/scanpy",
    "./single-cell/analysis/schard",
    "./single-cell/analysis/scvi-tools",
    "./single-cell/analysis/seurat",
    "./single-cell/integration/bbknn",
    "./single-cell/integration/harmony",
    "./single-cell/integration/scanorama",
    "./single-cell/integration/seurat-v5",
    "./single-cell/visualization/cellxgene",
    "./single-cell/visualization/cellxgene-census",
    "./spatial-omics/analysis/giotto",
    "./spatial-omics/analysis/spatialdata",
    "./spatial-omics/analysis/squidpy",
    "./spatial-omics/platforms/stereo-seq",
    "./spatial-omics/visualization/vitessce",
    "./structural-biology/chimerax-mcp",
    "./workflows/nextflow",
    "./workflows/snakemake"
  ]
}

Contents

What it installs

The manifest is a name and a version. 38 skills travel with it, and installing the plugin installs all of them — 1,681 tokens a session between them. Each is measured on its own page, and each can be installed alone.

Files

What ships with it

1 file beside marketplace.json#compbio in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

marketplace.json 7.1 KB

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

yesterday Changed · +2 lines 3445abac18b9
3d ago Changed · +34 lines e770b35a26db
8d ago Changed · +1 lines cb0270d3b4cf
1mo ago First seen · 9 lines scan A ad97ce58539b

Subscribe to this mod's changes

compbio is a plugin published in the GitHub repository CHENyiru3/AI-Skills-Collections (2 stars, last pushed 3d ago), licensed MIT. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-10-02.

Scientific

compbio next to 6 plugins from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
compbioCHENyiru3/AI-Skills-Collections	Plugin	2	3d ago	MIT	A	—	Claude Code
catalysis-scientistK-Dense-AI/scientific-agents	Plugin	246	1mo ago	MIT	A	—	Claude Code
hyphamycelium-cmbse/mycelium-hypha	Plugin	12	yesterday	Apache-2.0	A	—	Claude Code
r2g-skillsShenShan123/r2g-skills	Plugin	44	16d ago	MIT	B	—	Claude Code
aremaballarin/ccplugins	Plugin	4	19d ago	MIT	A	—	Claude Code
physical-sciencesKalarisLabs/research-agent-skills	Plugin	133	today	none	A	—	Claude Code
biorxiv-mcp-servercyanheads/biorxiv-mcp-server	Plugin	4	yesterday	none	A	—	Claude Code