# Consensus Clustering Analysis

Use when identifying stable sample subtypes from bulk expression matrices with...

- Repository: https://github.com/aipoch/medical-research-skills (2020 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-09-17
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -g -a claude-code -y`
Codex: `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -g -a codex -y`
Cursor: `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -g -a cursor -y`
Gemini CLI: `npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -g -a gemini-cli -y`

## Description

Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

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

# Consensus Clustering Analysis

## When to Use

Use this skill when you need to identify stable sample subtypes from a bulk expression matrix with `ConsensusClusterPlus`, compare candidate clustering settings with PAC, and export consensus matrix/CDF visualizations.

Do not use this skill for differential expression analysis, single-cell clustering, or non-expression tabular data.

## When to Read External Files

| Situation | File to Read | Purpose |
|-----------|--------------|---------|
| **Need algorithm details** | `references/algorithm.md` | Consensus clustering, PAC scoring, and preprocessing assumptions |
| **Need to run analysis** | `scripts/main.R` | Execute: `Rscript scripts/main.R --input_file ... --group_file ...` |
| **Encounter errors** | `references/troubleshooting.md` | Common errors and solutions |
| **Need CLI examples** | `references/cli-guide.md` | Detailed CLI usage examples with verified local runs |

---

## Usage

```bash
Rscript scripts/main.R \
  --input_file ./expression_matrix.csv \
  --group_file ./groups.csv \
  --disease_group case \
  --max_k 4 \
  --output_dir ./output/ \
  --gene_selection highly_variable \
  --top_n 5000 \
  --reps 1000 \
  --p_item 0.8 \
  --p_feature 1.0 \
  --timeout_seconds 3600 \
  --seed 42
```

---

## Arguments

The rest: https://github.com/aipoch/medical-research-skills/blob/HEAD/awesome-med-research-skills/Data Analysis/consensus-clustering-analysis/SKILL.md