geo-reanalysis

Guide reanalysis of GEO datasets with standard bioinformatics pipelines.

IndexedMIT★ 7

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Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/yejunbin-geo-reanalysis

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About

Guide reanalysis of GEO datasets with standard bioinformatics pipelines.

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What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

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~/.claude/skills/geo-reanalysis

What's inside

Skill name: geo-reanalysis
Description: Guide reanalysis of GEO datasets with standard bioinformatics pipelines.
License: MIT
Instructions: 39 lines in SKILL.md · view on GitHub

Files (1)

SKILL.md

SKILL.md (first lines)

# GEO Reanalysis

Reanalyze public GEO datasets for validation or hypothesis testing.

## Workflow

1. **Identify Dataset**
   - Search GEO for relevant series (GSE)
   - Check sample metadata and experimental design
   - Verify platform and annotation

2. **Download**
   - GEOquery (R) or GEOparse (Python)
   - Raw data (CEL, FASTQ) or processed matrices

3. **QC**
   - Sample clustering
   - Batch effect assessment
   - Outlier detection

4. **Analysis**
   - Differential expression (limma, DESeq2, edgeR)
   - Pathway enrichment
   - Survival analysis (if clinical data available)

5. **Validation**
   - Compare with original publication
   - Cross-validate with independent cohort

## Output

Save reanalysis log to `reanalyses/geo-<slug>.md` with:
- Dataset ID and description
- QC results
- Analysis parameters
- Key findings
- Comparison with original study

From yejunbin/darwin, MIT.

Signals

Stars: 7
Forks: 1
Open issues: 1
Last commit (this folder): May 8, 2026 (5 months ago)

From GitHub (fetched Oct 24, 2026).

Details

License: MIT
Repository: github.com/yejunbin/darwin
First seen: Oct 24, 2026
Last checked: Oct 24, 2026
Source: GitHub github-graphql

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geo-reanalysis skill. Agent Mart. https://agentmart.dev/skills/yejunbin-geo-reanalysis (last updated 2026-10-24)