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.
- Version
- 1.7
- License
- BSD-2-Clause license
- Compatibility
- Requires Python >=3.12, gget 0.30.8, and network access for remote queries. Use a separate Python 3.12/3.13 environment for optional Census dependencies. Local MUSCLE/DIAMOND need compatible binaries and OpenMP libraries; COSMIC downloads require an account.
Pinned to revision 68105dd992f1, 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/SKILL_CN.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.