Individual skill
gget
Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, 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.
skills/gget/SKILL.md
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- Repository last updated
- Nov 2, 2026
- License
- MIT
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- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
- claude-skills Repository topic
- claudecode Repository topic
- clinical-research Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- drug-discovery Repository topic
- data Derived category
- data-databases Derived category
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SKILL.mdcore · 11,253 bytesSKILL.mdcore · 11,253 bytesSKILL.mdcore · 11,253 bytesSKILL.mdcore · 11,253 bytesSKILL.mdcore · 11,253 bytesSKILL.mdcore · 11,253 bytesreferences/common_workflows.mddoc · 2,570 bytesreferences/database_info.mddoc · 13,641 bytesreferences/module_catalog.mddoc · 26,673 bytesreferences/module_reference.mddoc · 24,332 bytesreferences/workflows.mddoc · 9,807 bytesscripts/batch_sequence_analysis.pyruns · 6,717 bytesscripts/enrichment_pipeline.pyruns · 7,917 bytesscripts/gene_analysis.pyruns · 7,603 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 0.30.8 (reviewed 2026-09-30). For reproducible work, pin `gget==0.30.8`; 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