gget

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

1.59x

Quality

75%

Does it follow best practices?

Impact

99%

1.59x

Average score across 3 eval scenarios

Securityby

Risky

Do not use without reviewing

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/gget/SKILL.md

Evaluation results

100%

68%

Characterizing Differentially Expressed Genes from Lung Cancer Study

Enrichment analysis and expression queries

Criteria

Without context

With context

Pathway shortcut

100%

Ontology shortcut

100%

Transcription shortcut

100%

Diseases shortcut

100%

Celltypes shortcut

100%

archs4 tissue mode

100%

archs4 correlation mode

100%

Enrichment CSV outputs

100%

Expression CSV outputs

100%

Multiple databases covered

50%

100%

Script runs

100%

97%

12%

Building an Efficient Protein Sequence Comparison Pipeline

DIAMOND database reuse and BLAST database selection

Criteria

Without context

With context

DIAMOND db save

55%

100%

DIAMOND db reuse

100%

75%

BLAST swissprot database

100%

BLAST limit used

70%

100%

BLAST results saved

100%

DIAMOND results saved

100%

MUSCLE alignment used

60%

100%

Alignment output saved

100%

Pipeline log written

100%

Script runs

100%

29%

Building a Reproducible Gene Information Pipeline for Immune Gene Panel

Reproducible release pinning and batch size limits

Criteria

Without context

With context

Pinned release number

53%

100%

Release in config file

100%

Batch size limit acknowledged

100%

gget info called

25%

100%

pdb flag not used

100%

bgee orthologs single gene

50%

100%

bgee expression multiple genes

53%

100%

gget ref called

37%

100%

Outputs saved

100%

Script runs

100%

Batch config documented

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Characterizing Differentially Expressed Genes from Lung Cancer Study Building an Efficient Protein Sequence Comparison Pipeline Building a Reproducible Gene Information Pipeline for Immune Gene Panel

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