Skills geo-database

📦

geo-database

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

Explore GEO Gene Expression Data

Researchers need reliable access to public gene expression studies before analysis. This skill guides GEO search, download, metadata review, and transcriptomics workflows.

Supports: Claude Codex Code(CC)

📊 73 Adequate

📊 73 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/davila7-geo-database.md and its manifest at https://skillstore.io/api/skills/davila7-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/davila7-geo-database.md Signed manifest GET /api/skills/davila7-geo-database/manifest Signed lockfile GET /api/skills/davila7-geo-database/lockfile

Test it

Using "geo-database". Find human breast cancer GEO studies with available expression matrices.

Expected outcome:

Candidate series are grouped by accession, organism, platform, sample count, and publication metadata.
The response notes which records have series matrix files and which require supplementary downloads.

Using "geo-database". Prepare GSE123456 for local analysis.

Expected outcome:

The workflow identifies required Python libraries, the target data directory, expected GEO files, and metadata checks.
It also flags file size, sample grouping, platform annotation, and normalization questions before analysis.

Using "geo-database". Plan a meta-analysis across three GEO studies for TP53 expression.

Expected outcome:

The plan covers accession validation, platform compatibility, probe-to-gene mapping, expression extraction, and batch-effect review.
It includes citation reminders and a clear list of assumptions that need manual confirmation.

Security Audit

Safe

v15 • 7/9/2026 Open versioned report

The static scanner over-reported many Markdown code fence, identifier, and placeholder patterns. I confirmed only the FTP transport findings because the skill documents unauthenticated ftp:// downloads from NCBI; no prompt injection or credential exfiltration intent was found.

2

Files scanned

1,640

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 ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

references/geo_reference.md:541

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

references/geo_reference.md:551

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Medium

FTP protocol

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

The skill documents ftp:// access to NCBI GEO over unauthenticated FTP. Public data reduces impact, but downloaded content can be tampered with in transit; prefer HTTPS or checksum verification.

Risk Factors

🌐 Network access (26)

⚙️ External commands (39)

📁 Filesystem access (2)

SKILL.md:381 SKILL.md:378

🔑 Env variables (1)

Audited by: codex View Audit History →

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Open versioned report

Security Assessment

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https://skillstore.io/skills/davila7-geo-database/audits/15?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

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Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). geo-database security audit report (audit version 15) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-geo-database/audits/15

BibTeX citation

@techreport{davila7-davila7-geo-database-2026,
  author = {davila7},
  title = {geo-database security audit report (audit version 15)},
  institution = {Skillstore},
  year = {2026},
  number = {15},
  url = {https://skillstore.io/skills/davila7-geo-database/audits/15},
  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 15)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/davila7-geo-database/audits/15"
identifiers:
  - type: other
    value: "skillstore:davila7-geo-database:audit:15"
    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 Current

davila7-geo-database

Skillstore Score 73

Evidence Confidence High

Skillstore usage 14

Updated

2026-08-21

k-dense-ai-geo-database

Skillstore Score 71

Evidence Confidence High

Skillstore usage 10

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

41

Architecture

85

Maintainability

87

Content

73

Community

74

Spec Compliance

What You Can Build

Find datasets for a research question

Search GEO by organism, disease, technology, author, date, or accession and compare candidate studies.

Prepare expression data for analysis

Download series metadata, sample tables, platform annotations, and expression matrices into a local workflow.

Plan cross-study transcriptomics work

Review platform differences, sample metadata, gene mapping, and batch risks before meta-analysis.

Try These Prompts

Find Relevant GEO Studies

Find public GEO studies for [condition] in [organism]. Return accession IDs, titles, sample counts, platforms, and GEO record links.

Download One GEO Series

Download metadata and the expression matrix for [GSE accession] with GEOparse. Save files under [directory] and summarize sample groups.

Analyze Treatment Effects

Compare control and treatment samples in [GSE accession]. Explain normalization checks, differential expression steps, and outputs for significant genes.

Design a Meta-Analysis

Build a reproducible meta-analysis plan for these GEO series: [accessions]. Include platform harmonization, gene mapping, batch considerations, and citation checks.

Best Practices

Set an Entrez email and respect NCBI rate limits for every automated query.
Validate sample metadata, platform annotations, and expression scale before statistical analysis.
Record accession IDs, download dates, software versions, and source citations for reproducibility.

Avoid

Downloading entire directories before checking file sizes and available disk space.
Assuming GEO expression values are normalized without reviewing submission metadata.
Combining studies from different platforms without gene mapping and batch-effect controls.

Frequently Asked Questions

What is NCBI GEO?

GEO is a public repository for functional genomics data, including microarray and sequencing studies.

Does this skill download data automatically?

It provides workflows and commands. The user or agent must choose what to run and where to store files.

Which GEO accession types are covered?

The skill covers Series, Samples, Platforms, curated DataSets, and GEO Profiles.

Can it analyze RNA-seq data?

It can help locate RNA-seq studies and retrieve metadata, but raw RNA-seq processing may need separate tools.

What Python libraries does it use?

Examples use GEOparse for GEO records and Biopython Entrez for NCBI E-utilities queries.

How should I handle large datasets?

Check file sizes first, plan disk space, download incrementally, and cache data in a clear project directory.

Developer Details

Author

License

MIT

Skillstore revision

r1

Version notice

The author did not declare a version.

Repository

https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/geo-database

Ref

b959ebfd1043a07c0c4378ab94ca4342cb0259f5

Maintenance freshness

7/20/2026

Usage

8 downloads · 432 views

File structure

📁 references/

📄 geo_reference.md