Skills geo-database

📦

geo-database

Content revision r1 Safe 🌐 Network access⚙️ External commands📁 Filesystem access🔑 Env variables

Explore NCBI GEO Expression Data

Researchers often need reliable ways to find and reuse public gene expression datasets. This skill guides Claude, Codex, and Claude Code through NCBI GEO search, retrieval, parsing, and analysis workflows.

Supports: Claude Codex Code(CC)

📊 71 Adequate

📊 71 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "geo-database" from https://skillstore.io/skills/k-dense-ai-geo-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-geo-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/k-dense-ai-geo-database.md Signed manifest GET /api/skills/k-dense-ai-geo-database/manifest Signed lockfile GET /api/skills/k-dense-ai-geo-database/lockfile

Test it

Using "geo-database". Find GEO studies for breast cancer RNA-seq in humans.

Expected outcome:

A concise shortlist of candidate GEO Series, with organism, technology, sample context, and next steps for metadata review.

Using "geo-database". Explain what files I should download for GSE123456.

Expected outcome:

A plain-language comparison of series matrix, SOFT, MINiML, and supplementary files, with guidance on when each format is useful.

Using "geo-database". Plan a differential expression workflow for one GEO Series.

Expected outcome:

A stepwise analysis plan covering download, metadata checks, group assignment, expression extraction, quality control, testing, and citation notes.

Security Audit

Safe

v9 • 7/9/2026 Open versioned report

The skill is primarily documentation and examples for accessing public NCBI GEO data. I confirmed the plaintext FTP guidance as a medium concern because it can expose downloads to tampering. The remaining static findings are false positives involving public URLs, Markdown fences, placeholder keys, local data saves, and GEO identifiers.

2

Files scanned

1,645

Lines analyzed

7

Review items

0

False positives ignored

Capability review items (7)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

Medium

references/geo_reference.md:504

FTP protocol

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE{nnn}nnn/GSE{xxxxx}/

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

references/geo_reference.md:541

FTP protocol

ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM{nnn}nnn/GSM{xxxxx}/

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

references/geo_reference.md:551

FTP protocol

ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL{nnn}nnn/GPL{xxxxx}/

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

FTP protocol

wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

FTP protocol

wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

FTP protocol

wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Medium

FTP protocol

- **GEO FTP Site:** ftp://ftp.ncbi.nlm.nih.gov/geo/

The skill documents or recommends plaintext ftp:// GEO downloads. FTP lacks transport integrity and confidentiality, so users could receive tampered data on hostile networks.

Risk Factors

🌐 Network access (26)

⚙️ External commands (39)

📁 Filesystem access (2)

SKILL.md:384 SKILL.md:381

🔑 Env variables (1)

Audited by: codex View Audit History →

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Open versioned report

Security Assessment

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). geo-database security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-geo-database/audits/9

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-geo-database-2026,
  author = {K-Dense-AI},
  title = {geo-database security audit report (audit version 9)},
  institution = {Skillstore},
  year = {2026},
  number = {9},
  url = {https://skillstore.io/skills/k-dense-ai-geo-database/audits/9},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "geo-database security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
  - name: "K-Dense-AI"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/k-dense-ai-geo-database/audits/9"
identifiers:
  - type: other
    value: "skillstore:k-dense-ai-geo-database:audit:9"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended

davila7-geo-database

Skillstore Score 73

Evidence Confidence High

Skillstore usage 15

Updated

2026-09-09

K-Dense-AI Current

k-dense-ai-geo-database

Skillstore Score 71

Evidence Confidence High

Skillstore usage 11

Updated

2026-09-09

Skillstore Score

Why this score Evidence Confidence: High

41

Architecture

75

Maintainability

87

Content

70

Community

74

Spec Compliance

What You Can Build

Find disease expression studies

Search GEO for human disease datasets and summarize candidate GSE records for review.

Prepare expression matrices

Download a GEO Series, inspect sample metadata, and extract a matrix for downstream analysis.

Compare studies for a gene

Locate platform probes for a gene and compare expression summaries across selected studies.

Try These Prompts

Search for datasets

Find NCBI GEO datasets about [condition] in [organism]. Return likely GSE accessions, study types, sample counts, and why each result is relevant.

Retrieve study metadata

Use GEO guidance to review [GSE accession]. Summarize the title, organism, platform, samples, experimental design, and available file types.

Plan expression analysis

Create a workflow for downloading [GSE accession], extracting the expression matrix, separating control and treatment samples, and checking data quality.

Design a meta-analysis workflow

Plan a reproducible GEO meta-analysis for [gene or pathway] across [GSE accessions]. Include metadata harmonization, probe mapping, normalization checks, and statistical cautions.

Best Practices

Set an Entrez email address and respect NCBI rate limits for every automated query.
Check sample metadata, platform annotation, and processing methods before comparing expression values.
Cache large downloads locally and record dataset accessions, versions, and citations.

Avoid

Do not assume all GEO studies use comparable normalization or experimental design.
Do not download large supplementary files without checking disk space and file purpose.
Do not treat probe identifiers as gene symbols without platform-specific annotation mapping.

Frequently Asked Questions

What is NCBI GEO?

NCBI GEO is a public repository for gene expression and functional genomics datasets.

Can this skill download GEO files?

Yes. It provides workflows for GEOparse, E-utilities, and direct file downloads from GEO locations.

Does it support RNA-seq and microarray data?

Yes. The guidance covers GEO study searches and file handling for both sequencing and array experiments.

Does it perform final statistical interpretation?

No. It can outline analysis steps, but results need statistical and biological review.

What tools does it expect?

The examples use Python libraries such as GEOparse, Biopython, pandas, scipy, and visualization packages.

How should I handle API keys?

Use NCBI API keys only when needed, store them securely, and avoid committing them to shared files.

Developer Details

Author

License

Unknown

Skillstore revision

r1

Version notice

The author did not declare a version.

Repository

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

Ref

26421118b848d9f1efc0aa169d8a7a9e7e0a877e

Maintenance freshness

7/18/2026

Usage

8 downloads · 220 views

File structure

📁 references/

📄 geo_reference.md

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