geo-database

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

1.02x

Quality

66%

Does it follow best practices?

Impact

80%

1.02x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Optimize this skill with Tessl

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

Evaluation results

100%

10%

GEO Dataset Catalog for Neurodegeneration Research

GEO search with E-utilities and rate limiting

Criteria

Without context

With context

biopython install

100%

Entrez.email set

100%

usehistory param

100%

rate limiting present

100%

correct sleep value

100%

gds database used

100%

esummary called

100%

handles closed

100%

output JSON saved

100%

Organism search field

100%

66%

-3%

Differential Expression Analysis of Colorectal Cancer GEO Dataset

GEOparse expression analysis with differential expression

Criteria

Without context

With context

GEOparse import

100%

20%

uv install GEOparse

destdir parameter

100%

pivot_samples used

log2 transform check

100%

log2 threshold check

62%

100%

ttest_ind used

100%

fdr_bh correction

100%

q_value threshold

100%

fold change threshold

100%

results saved to CSV

100%

74%

-2%

Cross-Study Expression Analysis of a Candidate Biomarker

Multi-dataset batch processing with platform annotation mapping

Criteria

Without context

With context

GEOparse primary library

100%

uv pip install

100%

destdir for caching

100%

platform annotation access

100%

filters unmapped probes

100%

Gene Symbol column

100%

batch summary CSV

100%

visualization saved

100%

plot dpi=300

bbox_inches tight

100%

error handling per dataset

100%

pivot_samples extraction

Repository: K-Dense-AI/claude-scientific-skills
Commit: 71add64

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

Table of Contents

GEO Dataset Catalog for Neurodegeneration Research Differential Expression Analysis of Colorectal Cancer GEO Dataset Cross-Study Expression Analysis of a Candidate Biomarker

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