Agent skill · research science · k-dense-ai
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Why this skill is useful
Provides access to niche bioinformatics databases and specific query patterns that the AI wouldn't reliably generate on its own.
What it needs
Requires gget, python installed locally. About 4k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
gget Overview gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions. Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin gget==0.30.5; for broken upstream database adapters, update gget after checking release notes. Installation Install gget in a clean virtual environment to avoid conflicts: Quick Start Basic usage pattern for all modules: Most modules return: Command-line: JSON (default) or CSV with -csv flag Python: DataFrame or dictionary Common flags across modules: -o/--out: Save results to file -q/--quiet: Suppress progress information -csv: Return CSV format (command-line only) Python argument names generally match long CLI options without leading dashes. For example, --censusversion becomes censusversion=.... Use gget <module> --help for the exact current signature. Module Categories gget exposes 23 modules in six categories. Parameters, CLI and Python examples, and return shapes for every one are in references/modulecatalog.md; fuller per-parameter documentation is in references/modulereference.md. Category Modules --- --- 1. Reference & gene information ref (Ensembl reference downloads), search (gene search), info (gene/transcript detail), seq (nucleotide and protein sequences) 2. Sequence analysis & alignment blast, blat, muscle (multiple alignment), diamond (local alignment) 3. Structural & protein analysis pdb (structures and metadata), alphafold (structure prediction), elm (linear motifs) 4. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/gget