What is alterlab-bioinformatics?

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.

Use it for genomics, proteomics, single-cell analysis, sequence searches, protein modelling, gene-expression data, and biological data processing.

It supports specialised biology workflows that are difficult to perform with general-purpose coding tools alone.

alterlab-bioinformatics — Plugin for Claude Code by AlterLab-IEU

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/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.

README.md

[![agentmods](https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics/github.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/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/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics"><img src="https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-bioinformatics.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 5,339 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

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 1mo 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": "3.0.1",
  "author": {
    "name": "AlterLab @ Izmir University of Economics",
    "url": "https://github.com/AlterLab-IEU"
  },
  "homepage": "https://github.com/AlterLab-IEU/AlterLab-Academic-Skills",
  "license": "MIT AND Apache-2.0 AND GPL-2.0 AND GPL-3.0",
  "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 — 5,339 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.

marketplace.json 27 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.

1mo ago Changed a9dead208c77
1mo 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 (78 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 AI Scientific academic-research anthropic bioinformatics data-science prompt-engineering research-tools

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alterlab-bioinformatics