์Šคํ‚ฌ gget
๐Ÿงฌ

gget

์•ˆ์ „ ๐ŸŒ ๋„คํŠธ์›Œํฌ ์ ‘๊ทผ๐Ÿ“ ํŒŒ์ผ ์‹œ์Šคํ…œ ์•ก์„ธ์Šค

Query genomic databases for gene info and sequences

๋˜ํ•œ ๋‹ค์Œ์—์„œ ์‚ฌ์šฉํ•  ์ˆ˜ ์žˆ์Šต๋‹ˆ๋‹ค: davila7

gget provides unified access to 20+ genomic databases through a simple CLI or Python interface. Query gene information, retrieve sequences, perform BLAST searches, and run enrichment analysis without managing multiple API connections.

์ง€์›: Claude Codex Code(CC)
๐Ÿฅˆ 77 ์‹ค๋ฒ„
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"gget" ์‚ฌ์šฉ ์ค‘์ž…๋‹ˆ๋‹ค. Search for BRCA1 gene in human

์˜ˆ์ƒ ๊ฒฐ๊ณผ:

  • Found: ENSG00000012048 (BRCA1)
  • Description: BRCA1 DNA repair associated
  • UniProt ID: P38398
  • Chromosome: 17q21.31
  • Biotype: protein coding

"gget" ์‚ฌ์šฉ ์ค‘์ž…๋‹ˆ๋‹ค. Get tissue expression for ACE2

์˜ˆ์ƒ ๊ฒฐ๊ณผ:

  • Kidney: median expression 245.3
  • Testis: median expression 189.7
  • Small intestine: median expression 156.2
  • Bladder: median expression 98.4

๋ณด์•ˆ ๊ฐ์‚ฌ

์•ˆ์ „
v4 โ€ข 1/17/2026

This is legitimate bioinformatics software. All 614 static findings are false positives: markdown code fences were misidentified as Ruby shell execution, hardcoded URLs are public genomic databases (Ensembl, UniProt, NCBI), cryptographic patterns are data integrity checksums, and the critical heuristic is standard bioinformatics behavior (network queries to public APIs + local file operations for results).

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๐ŸŒ ๋„คํŠธ์›Œํฌ ์ ‘๊ทผ (2)
references/database_info.md:22 SKILL.md:866-868
๐Ÿ“ ํŒŒ์ผ ์‹œ์Šคํ…œ ์•ก์„ธ์Šค (3)
scripts/gene_analysis.py:55-61 scripts/enrichment_pipeline.py:24-25 scripts/batch_sequence_analysis.py:97-98
๊ฐ์‚ฌ์ž: claude ๊ฐ์‚ฌ ์ด๋ ฅ ๋ณด๊ธฐ โ†’

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๋งŒ๋“ค ์ˆ˜ ์žˆ๋Š” ๊ฒƒ

Quick gene lookups

Rapidly retrieve gene information, sequences, and annotations from Ensembl, UniProt, and NCBI during research exploration.

Enrichment analysis

Run gene ontology and pathway enrichment on gene lists to identify biological patterns and functional associations.

Sequence comparison

Perform BLAST searches and retrieve protein structures for sequence analysis and comparison tasks.

์ด ํ”„๋กฌํ”„ํŠธ๋ฅผ ์‚ฌ์šฉํ•ด ๋ณด์„ธ์š”

Basic gene search 
Use gget to search for the gene TP53 in human and return its Ensembl ID, description, and UniProt ID.
Sequence retrieval 
Retrieve the nucleotide and protein sequences for Ensembl gene ENSG00000139618 in FASTA format using gget.
BLAST search 
Run a BLAST search using gget to find similar sequences to 'MSEQWKAVLFPLLLAAATSL...'. Use the nr database and return top 5 hits.
Enrichment analysis 
Run gget enrichr on the gene list ['TP53', 'BRCA1', 'MDM2', 'CDKN1A'] against KEGG Pathways database and show top 10 enriched terms.

๋ชจ๋ฒ” ์‚ฌ๋ก€

  • Keep gget updated to match changing database structures
  • Use the -csv flag for CLI output to simplify parsing
  • Limit large queries to avoid server timeout errors

ํ”ผํ•˜๊ธฐ

  • Running thousands of queries without rate limiting
  • Using unreleased database versions in reproducible workflows
  • Skipping result validation when downstream analysis depends on data quality

์ž์ฃผ ๋ฌป๋Š” ์งˆ๋ฌธ

What databases does gget query?
gget queries 20+ databases including Ensembl, UniProt, NCBI, PDB, KEGG, AlphaFold, and ARCHS4.
Does gget require authentication?
No, gget queries public genomic databases that do not require API keys for standard usage.
Can I use gget in Python scripts?
Yes, gget works as both a CLI tool and a Python package. Import gget and call gget.module() directly.
How does gget handle rate limits?
gget includes built-in rate limiting. For high-volume queries, consider adding delays between requests.
What species are supported?
gget supports all species in Ensembl including human, mouse, rat, fly, worm, yeast, and many more.
How accurate are enrichment results?
Enrichr provides statistical enrichment using hypergeometric testing. Adjust p-value cutoffs based on your analysis needs.

๊ฐœ๋ฐœ์ž ์„ธ๋ถ€ ์ •๋ณด

์ž‘์„ฑ์ž

K-Dense-AI

๋ผ์ด์„ ์Šค

BSD-2-Clause license

๋ฆฌํฌ์ง€ํ† ๋ฆฌ

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/gget

์ฐธ์กฐ

main

ํŒŒ์ผ ๊ตฌ์กฐ

๐Ÿ“ references/

๐Ÿ“„ database_info.md

๐Ÿ“„ module_reference.md

๐Ÿ“„ workflows.md

๐Ÿ“ scripts/

๐Ÿ“„ batch_sequence_analysis.py

๐Ÿ“„ enrichment_pipeline.py

๐Ÿ“„ gene_analysis.py

๐Ÿ“„ evaluation_output.json

๐Ÿ“„ SKILL.md