Individual skill

wgcna-analysis

Use when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules with WGCNA, correlating modules with traits, and exporting module-level plots and gene tables. NOT for single-cell RNA-seq, differential expression testing, methylation analysis, or datasets that are too small for WGCNA after quality control.

awesome-med-research-skills/Data Analysis/wgcna-analysis/SKILL.md

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Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91

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Matches the observed repository HEAD: Yes
Scanner rules are current: No
Repository scan complete: No
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Observed behavior: Not checked yet
Last checked: Nov 9, 2026

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Repository context

Repository stars (not skill ratings): 2,043
Repository last updated: Sep 17, 2026
License: MIT

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
data-visualization Repository topic
differential-expression Repository topic
genomics Repository topic
medical Repository topic
testing Derived category

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files

SKILL.mdcore · 11,647 bytes
SKILL.mdcore · 11,647 bytes
SKILL.mdcore · 11,647 bytes
SKILL.mdcore · 11,647 bytes
eval_report_wgcna-analysis_result.jsonasset · 15,848 bytes
references/algorithm.mddoc · 4,314 bytes
references/cli-guide.mddoc · 11,408 bytes
references/troubleshooting.mddoc · 5,396 bytes
scripts/chunk_io.Rasset · 5,576 bytes
scripts/functions.Rasset · 2,088 bytes
scripts/io.Rasset · 2,576 bytes
scripts/main.Rruns · 4,676 bytes
scripts/plotting.Rasset · 7,804 bytes
scripts/run_analysis.Rasset · 5,407 bytes
scripts/utils.Rasset · 4,358 bytes
scripts/wgcna_core.Rasset · 3,605 bytes
scripts/wgcna_selection.Rasset · 4,802 bytes
tests/data/expression.csvasset · 690,641 bytes
tests/data/group.csvasset · 299 bytes
tests/validate_outputs.Rruns · 1,225 bytes

Read excerpt

> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

# WGCNA Analysis

## When to Read External Files

**AI Agent: This section tells you when to read additional files.**

| Situation | File to Read | Purpose |
|-----------|--------------|---------|
| **Need algorithm details** | `references/algorithm.md` | WGCNA workflow, filtering strategy, statistics, assumptions |
| **Need to run analysis** | `scripts/main.R` | Execute: `Rscript scripts/main.R --input_file ... --group_file ...` |
| **Encounter errors** | `references/troubleshooting.md` | Common errors, causes, and fixes |
| **Need CLI examples** | `references/cli-guide.md` | Complete command examples for common scenarios |
| **Need conversion audit details** | `references/diagnosis-report.md` | Skill readiness assessment and remediation summary |