Medical Research Agent Skills is a library of agent instructions for medical and biomedical research, covering evidence analysis, study protocol design, data analysis, and academic writing. Researchers use it to guide compatible coding agents through common scientific workflows. The catalogue contains many of the library's skills and commands.
Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/aipoch/medical-research-skillsnpx agentmods add skills/aipoch/medical-research-skills/hierarchical-clustering-plotWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/aipoch/medical-research-skills/hierarchical-clustering-plot)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/hierarchical-clustering-plot"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/hierarchical-clustering-plot/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/hierarchical-clustering-plot"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/hierarchical-clustering-plot.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00074 | $0.02868 |
| Opus 5 | $0.00037 | $0.01434 |
| Sonnet 5 | $0.00015 | $0.00574 |
| Haiku 4.5 | $0.00007 | $0.00287 |
Grade A, and why
hierarchical-clustering-plot scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 279 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Hierarchical Clustering Plot
When to Use
Use this skill when you need a sample-level hierarchical clustering dendrogram from a bulk expression matrix and a sample annotation table.
- Good fits: sample QC, batch inspection, sample similarity assessment, checking whether annotated sample groups cluster as expected.
- Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity.
- Not for: differential expression testing, gene clustering heatmaps, single-cell clustering workflows.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
Distance calculation, linkage rules, and clustering assumptions |
| Need to run analysis or inspect CLI entrypoint behavior | scripts/main.R |
Execute the workflow and inspect argument parsing, defaults, required flags, and sourced modules |
| Need workflow implementation details | scripts/run_analysis.R |
See orchestration order, temp workspace handling, and output generation |
| Need logging or warning behavior | scripts/logging_utils.R |
See standardized console log formatting and memory usage messages |
| Need file or parameter validation details | scripts/validation_utils.R |
See path checks, output-directory checks, and scalar validation |
| Need timeout, temp workspace, or session info behavior | scripts/runtime_utils.R |
See timeout control, temp cleanup, output copying, and session-info export |
| Need expression/group input handling | scripts/input_functions.R |
See CSV loading, sample matching, and label extraction |
| Need clustering logic | scripts/clustering_functions.R |
See distance calculation and hclust() generation |
| Need output-writing logic | scripts/output_utils.R |
See CSV export and PDF rendering |
| Encounter errors, warnings, or unexpected clustering patterns | references/troubleshooting.md |
Common failures, warning follow-up, and interpretation guidance |
| Need CLI examples or common parameter combinations | references/cli-guide.md |
Detailed command patterns for standard, variant, and test runs |
| Need example input files or schema-concrete fixtures | tests/data/ |
Inspect sample CSV layouts for expression and group inputs |
| Need expected output names or artifact formats | ## Output Files and references/cli-guide.md |
Confirm the files the workflow writes and inspect documented example previews |
| Need to run regression tests | tests/run_tests.R |
Execute the automated test suite |
| Need exact test assertions or edge cases | tests/testthat/test-clustering.R |
Inspect validation, reproducibility, and output checks |
What ships with it
17 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- DESCRIPTION 378 B
- eval_report_hierarchical-clustering-plot_result.json 12 KB
- references/algorithm.md 2.5 KB
- references/cli-guide.md 4.5 KB
- references/troubleshooting.md 5.4 KB
- scripts/clustering_functions.R 1.2 KB
- scripts/input_functions.R 4.1 KB
- scripts/logging_utils.R 1.0 KB
- scripts/main.R 3.8 KB
- scripts/output_utils.R 1.3 KB
- scripts/run_analysis.R 3.7 KB
- scripts/runtime_utils.R 1.6 KB
- scripts/validation_utils.R 1.8 KB
- tests/data/sample_expression_matrix.csv 10 KB
- tests/data/sample_groups.csv 653 B
- tests/run_tests.R 1.4 KB
- tests/testthat/test-clustering.R 6.1 KB
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 279 lines · 74 tokens per session scan A 5ba8faebcdf8
hierarchical-clustering-plot is a skill published in the GitHub repository aipoch/medical-research-skills (1,855 stars, last pushed 1mo ago), licensed MIT. It adds 74 tokens to every session and 2,868 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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bedgraph-file-format-manipulation
Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for downstream statistical comparison or peak detection.