agentmods.dev

alterlab-bioinformatics

alterlab-bioinformatics is a plugin for Claude Code from AlterLab-IEU/AlterLab-Academic-Skills. Its manifest loads nothing; the 38 skills it bundles cost 5,310 tokens per session together, scanned A, original, MIT.

A collection of tools for studying biological data such as DNA, proteins, and individual cells. It covers tasks including sequence analysis, gene-expression analysis, protein structure prediction, and processing sequencing data.

In plain words
What is it for?
Use it for genomics, proteomics, single-cell analysis, sequence searches, protein modelling, gene-expression data, and biological data processing.
Why use it?
It supports specialised biology workflows that are difficult to perform with general-purpose coding tools alone.

Plugin for Claude Code

Written for Claude Code: a Claude Code plugin manifest.

not rated 64 +2 yesterday A scan tokens not measured original MIT
View the source file AlterLab-IEU/AlterLab-Academic-Skills alterlab-ieu.github.io
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.

Claude Code
/plugin marketplace add AlterLab-IEU/AlterLab-Academic-Skills
agentmods
npx agentmods add plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics
Clone the repo
git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

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.

agentmods badge for alterlab-bioinformatics

README.md
[![agentmods](https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics.svg)](https://agentmods.dev/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics)
Your own site
<a href="https://agentmods.dev/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics"><img src="https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics.svg" alt="Measured on agentmods" 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 5,310 tokens a session between them.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Security

Grade A, and why

alterlab-bioinformatics 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 3d ago.

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#alterlab-bioinformatics · 61 lines

What it actually says

{
  "name": "alterlab-bioinformatics",
  "source": "./skills/bioinformatics",
  "description": "Genomics, proteomics, and single-cell analysis (Scanpy, BioPython, pysam, ESM) (38 skills)",
  "version": "2.6.1",
  "author": {
    "name": "AlterLab @ Izmir University of Economics",
    "url": "https://github.com/AlterLab-IEU"
  },
  "homepage": "https://github.com/AlterLab-IEU/AlterLab-Academic-Skills",
  "license": "MIT",
  "category": "science",
  "keywords": [
    "genomics",
    "proteomics",
    "single-cell",
    "scanpy",
    "biopython"
  ],
  "strict": false,
  "skills": [
    "./alterlab-alphafold",
    "./alterlab-anndata",
    "./alterlab-arboreto",
    "./alterlab-biopython",
    "./alterlab-bioservices",
    "./alterlab-blast",
    "./alterlab-boltz",
    "./alterlab-borzoi",
    "./alterlab-cellxgene",
    "./alterlab-chai",
    "./alterlab-cobrapy",
    "./alterlab-deeptools",
    "./alterlab-esm",
    "./alterlab-etetoolkit",
    "./alterlab-flowio",
    "./alterlab-gget",
    "./alterlab-glycoengineering",
    "./alterlab-histolab",
    "./alterlab-lamindb",
    "./alterlab-ligandmpnn",
    "./alterlab-neuropixels",
    "./alterlab-nf-core-sarek",
    "./alterlab-pathml",
    "./alterlab-phylogenetics",
    "./alterlab-proteinmpnn",
    "./alterlab-pydeseq2",
    "./alterlab-pyopenms",
    "./alterlab-pysam",
    "./alterlab-qiime2-amplicon",
    "./alterlab-rfdiffusion",
    "./alterlab-rnaseq-quant",
    "./alterlab-scanpy",
    "./alterlab-scgpt",
    "./alterlab-scikit-bio",
    "./alterlab-scvelo",
    "./alterlab-scvi-tools",
    "./alterlab-squidpy-spatial",
    "./alterlab-tiledbvcf"
  ]
}
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 — 5,310 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#alterlab-bioinformatics 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.

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.

  1. 3d ago First seen · 61 lines scan A 61434a82dd73

Subscribe to this mod's changes

alterlab-bioinformatics is a plugin published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (64 stars, last pushed yesterday), 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 2026-09-03.

Data and AIScientificacademic-researchanthropicbioinformaticsdata-scienceprompt-engineeringresearch-tools
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