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.
- Version
- 1.5
- License
- BSD-2-Clause license
- Compatibility
- Requires Python >=3.8 and gget 0.30.5-compatible APIs. Optional setup modules may install scientific dependencies that lag the newest Python releases; use Python 3.9 or 3.10 if `gget setup cellxgene` or `gget setup alphafold` fails.
Pinned to revision 70a605012eee, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/gget/SKILL.md
- skills/gget/references/common_workflows.md
- skills/gget/references/database_info.md
- skills/gget/references/module_catalog.md
- skills/gget/references/module_reference.md
- skills/gget/references/workflows.md
- skills/gget/scripts/batch_sequence_analysis.py
- skills/gget/scripts/enrichment_pipeline.py
- skills/gget/scripts/gene_analysis.py
Every link opens the file at its source, pinned to the revision this page describes.