consensus-clustering-analysis

1> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
2 
3# Consensus Clustering Analysis
4 
5## When to Use
6 
7Use 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.
8 
9Do not use this skill for differential expression analysis, single-cell clustering, or non-expression tabular data.
10 
11## When to Read External Files
12 
13| Situation | File to Read | Purpose |
14|-----------|--------------|---------|
15| **Need algorithm details** | `references/algorithm.md` | Consensus clustering, PAC scoring, and preprocessing assumptions |
16| **Need to run analysis** | `scripts/main.R` | Execute: `Rscript scripts/main.R --input_file ... --group_file ...` |
17| **Encounter errors** | `references/troubleshooting.md` | Common errors and solutions |
18| **Need CLI examples** | `references/cli-guide.md` | Detailed CLI usage examples with verified local runs |
19 
20---
21 
22## Usage
23 
24```bash
25Rscript scripts/main.R \
26  --input_file ./expression_matrix.csv \
27  --group_file ./groups.csv \
28  --disease_group case \
29  --max_k 4 \
30  --output_dir ./output/ \
31  --gene_selection highly_variable \
32  --top_n 5000 \
33  --reps 1000 \
34  --p_item 0.8 \
35  --p_feature 1.0 \
36  --timeout_seconds 3600 \
37  --seed 42
38```
39 
40---
41 
42## Arguments
43 
44| Short | Long | Type | Default | Description |
45…