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gget Bioinformatics Query Helper

A skill that teaches Claude to query 20+ genomic databases quickly through the gget CLI and Python API.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

Guides Claude in using gget to look up Ensembl gene/transcript details, run BLAST/BLAT and DIAMOND alignments, fetch PDB or AlphaFold structures, run Enrichr enrichment, query disease/drug/mutation data (OpenTargets, COSMIC, cBioPortal), pull CELLxGENE single-cell data, and download viral sequences. It includes a table mapping all 23 modules into 6 categories, shared flags (-o, -csv, -q), output formats (JSON/CSV/FASTA/PDB/AnnData), and per-area best practices.

Who it's for

  • Researchers tired of hopping between genomic database websites for routine lookups
  • Grad students and analysts who need reproducibility: pinned gget==0.30.5 and saved outputs
  • NGS analysts preparing reference files for kallisto or alignment pipelines

Example uses

  • "Get BRCA1 gene info plus its protein sequence and save as CSV" → gget search → gget info → gget seq
  • "Run GO/KEGG enrichment on this gene list" → gget enrichr with database shortcuts
  • "Check PDB first, and if no structure exists predict it" → gget pdb, then gget setup alphafold and gget alphafold

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/gget/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/gget folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/gget/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/gget ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/gget ~/.claude/skills/
  4. Verify the bundled docs exist: ls ~/.claude/skills/gget/references
  5. Create a Python 3.9–3.10 virtual environment and install the tool: uv venv .venv && source .venv/bin/activate && uv pip install "gget==0.30.5"
  6. Confirm with gget --help; if you plan to use alphafold, cellxgene, or elm, run gget setup <module> once.
  7. Restart Claude Code and try a prompt like "Use gget to look up TP53 gene info."
View source on GitHub ↗License: MIT