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gget Bioinformatics Database Queries

Query 20+ bioinformatics databases — gene info, BLAST/BLAT, AlphaFold structures, expression and disease data — with single CLI or Python calls.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 7/10Last updated: Aug 9, 2026

What it does

gget unifies 20+ genomics resources (Ensembl, UniProt, PDB, AlphaFold, Enrichr, OpenTargets, COSMIC, CELLxGENE, ARCHS4 and more) behind one consistent interface. This skill teaches Claude the 23 gget modules grouped into six categories — reference/gene info, sequence analysis and alignment, structural/protein analysis, expression and disease data, viral and mouse specificity, plus utility modules — and how to pick the right command for a given question.

  • Covers both CLI and Python usage plus shared flags (-o, -q, -csv)
  • Per-module parameters and return shapes are delegated to files under references/
  • Emphasizes reproducibility: pin gget==0.30.5, use virtual environments, rate-limit large API queries
  • Recommends keeping COSMIC/OpenAI credentials in environment variables rather than in notebooks or logs

Who it's for

  • Life-science researchers and grad students who need quick gene/protein lookups
  • Anyone who prefers conversational exploration over writing long scripts
  • Users cross-checking single-cell, expression, and disease-association data across databases
  • Less suitable if you need heavy batch processing or advanced BLAST tuning — biopython fits better there

Examples

  1. Characterize a gene: "Get the Ensembl ID, transcripts, and protein sequence for BRCA1" → chained gget search → gget info → gget seq.
  2. Structure lookup then prediction: "Check PDB first; if no structure exists, predict it" → gget pdb, then gget setup alphafold and gget alphafold -r.
  3. Expression + enrichment: "Run GO enrichment on this gene list and show tissue expression" → combine gget enrichr and gget archs4, saving results as CSV.

· · · Install guide · · ·

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 skill repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy only the gget skill: cp -r scientific-agent-skills/skills/gget ~/.claude/skills/
  4. Use Python 3.9 or 3.10 and create a virtual environment: python3 -m venv .venv && source .venv/bin/activate
  5. Install the pinned version: pip install "gget==0.30.5"
  6. Verify the install: gget --version
  7. If you plan to use alphafold, cellxgene, or elm, run the one-time gget setup <module> first.
  8. Restart Claude Code and try a prompt like "Use gget to look up BRCA1 gene info".
  9. For COSMIC or the gpt module, store credentials in environment variables — never paste them into code, notebooks, or logs.
View source on GitHub ↗License: MIT