Individual skill
gget
Queries 20+ bioinformatics databases and analysis services through the gget CLI and Python package, covering Ensembl gene search, info and sequences (ref, search, info, seq), BLAST, BLAT, MUSCLE, DIAMOND, PDB, AlphaFold, ELM, ARCHS4, CELLxGENE, Enrichr, Bgee, OpenTargets, cBioPortal, COSMIC, viral sequence downloads (virus), and 8cube mouse specificity and expression data. Use when looking up gene or transcript details, running a quick BLAST/BLAT search, fetching AlphaFold or PDB structures, running enrichment analysis on a gene list, downloading viral sequences with filters, or exploring disease and drug associations interactively. Not for batch processing or fine-grained BLAST control (use biopython) or multi-database Python pipelines (use bioservices).
plugins/KalarisLabs/research-agent-skills/skills/gget/SKILL.md
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- Network or broad shell
- Last checked
- Nov 4, 2026
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- 1,532
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
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- bioinformatics-databases,-ensembl,-blast,-alphafold,-gene-lookup Declared skill tag
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SKILL.mdcore · 10,047 bytesSKILL.mdcore · 10,047 bytesSKILL.mdcore · 10,047 bytesSKILL.mdcore · 10,047 bytesreferences/common_workflows.mddoc · 3,185 bytesreferences/database_info.mddoc · 12,223 bytesreferences/module_catalog.mddoc · 23,578 bytesreferences/module_reference.mddoc · 21,573 bytesreferences/workflows.mddoc · 26,073 bytesscripts/batch_sequence_analysis.pyruns · 6,119 bytesscripts/enrichment_pipeline.pyruns · 7,201 bytesscripts/gene_analysis.pyruns · 6,297 bytes
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# 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:
```bash
# Reproducible install targeting this skill