Consensus Clustering Analysis
Use when identifying stable sample subtypes from bulk expression matrices with...
Install
npx skills add aipoch/medical-research-skills --skill consensus-clustering-analysis -g -a claude-code -y- Repository
- aipoch/medical-research-skills2k
- Category
- Engineering
- Updated
- 2mo ago
- License
- MIT
- Context cost
- Mediumabout 1,874 tokens
- Runs scripts
- No, instructions only
What it does
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.
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
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
