NCBI GEO (Claude Skill)

NCBI GEO access via GEOparse and E-utilities.

Type	Claude Skill
Supplier	jaechang-hits (community OSS, CC BY 4.0)
Availability	GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing	Free / OSS (MIT)
Capabilities	Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

• Claude Code — clone and load as a plugin:

  git clone https://github.com/jaechang-hits/SciAgent-Skills
  

  Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.

• Manual / other agents — point the agent at the skill file directly:

  cp -r SciAgent-Skills/skills/genomics-bioinformatics/databases/geo-database ~/.claude/skills/
  

  The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.

Primary use cases: NCBI GEO access via GEOparse and E-utilities.

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: MIT. The skill directory upstream is skills/genomics-bioinformatics/databases/geo-database.

Sources

• jaechang-hits/SciAgent-Skills
• skills/genomics-bioinformatics/databases/geo-database/SKILL.md

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