gget Genomic Lookups
Quick bioinformatics lookups with the gget CLI and Python package: Ensembl IDs, sequences, BLAST-style searches, enrichment, and reproducible evidence logs.
- What
- Quick bioinformatics lookups with the gget CLI and Python package: Ensembl IDs, sequences, BLAST-style searches, enrichment, and reproducible evidence logs.
- Cost
- Free
- Needs
- Use "gget Genomic Lookups" with your Muse.
- Install
- Copy the installer prompt below into your Muse — your agent does the rest.
Curated by Skill Harbor: a quick-lookup workflow for bioinformatics built on the gget CLI and Python package. Find Ensembl IDs, gene metadata, transcript details, and sequences; run quick BLAST or BLAT lookups without building a full local pipeline; fetch reference genome links and annotations from Ensembl; query protein structure, pathway, cancer, expression, and disease-association modules through a single interface; and create a reproducible first-pass evidence log before moving to heavier tools like Biopython, Snakemake, Nextflow, BLAST+, or database-specific clients. Installs into a clean Python environment (venv or uv), upgrades before relying on older environments, and uses one CLI shape (gget module arguments options) plus one Python shape for everything. By @affaan-m, listed here with credit to its creator. From the affaan-m/ECC repository (MIT). Honest caveats: a first-pass tool, not a production pipeline; upstream databases change over time, so re-check module docs; never use for regulated clinical interpretation, high-throughput production, or anything needing fine-grained control over database versions. Skill Harbor never reviews the code, review it yourself before use.
Version:
Install
Copy the install package below, then paste it into MuseThe install prompt below already includes the vetting steps: your agent follows the community checklist before installing anything with executable code. Want more?
Use "gget Genomic Lookups" with your Muse. 1. Open the skill: https://github.com/affaan-m/ECC/blob/main/skills/scientific-pkg-gget/SKILL.md and copy the full SKILL.md text. 2. Paste it into a chat with Muse and add: "Look up [gene] in Ensembl" or "Run a quick BLAST-style search for [sequence]" or "Fetch the reference genome for [organism]." 3. Install gget in a clean Python environment first (python -m venv .venv, pip install --upgrade gget) and upgrade before relying on an older install. Tip: use it for the reproducible first-pass evidence log, then move to Biopython, Snakemake, or Nextflow when the task outgrows quick lookups. Safety: a skill is plain-text instructions; it runs nothing by itself. Never use for regulated clinical interpretation. Keep patient or clinical data out of any chat.
Saved to your recent installs. Find it anytime on /connect.
Questions
How do I install a build?
Every product page includes a copy-paste install prompt. Paste it into your Muse and it sets the build up for you — no manual configuration.
Where does my money go?
Straight to the seller. Skill Harbor never processes payments: checkout happens on the seller’s own page, usually Stripe.
What does the ✓ next to a creator’s name mean?
It means we confirmed the identity of the person behind the listing. It says nothing about the code itself — always check a build before installing it.