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
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add aipoch/medical-research-skills --skill sample-group-sankey-plotgit clone --depth 1 https://github.com/aipoch/medical-research-skillsWrote 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/sample-group-sankey-plot)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/sample-group-sankey-plot"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/sample-group-sankey-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/sample-group-sankey-plot"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/sample-group-sankey-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 | $0.00064 | $0.02318 |
| Opus 5 | $0.00032 | $0.01159 |
| Sonnet 5 | $0.00013 | $0.00464 |
| Haiku 4.5 | $0.00006 | $0.00232 |
Grade A, and why
sample-group-sankey-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 11d 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 — 262 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Sample Group Sankey Plot
Builds a reproducible Sankey/alluvial visualization from a tabular sample annotation file and exports the selected annotations, lodes-format table, plot PDF, and session metadata.
Input Validation
This skill accepts: a sample annotation table in CSV or TSV format where rows are samples and selected columns are categorical stages (e.g., risk group, response status, subtype, cohort label). At least 2 stage columns are required.
If the user's request does not involve generating a Sankey or alluvial flow diagram from categorical sample annotations — for example, asking to visualize a gene regulatory network, plot continuous-value trajectories, analyze pathway flow, or process non-tabular data — do not proceed with the workflow. Instead respond:
"sample-group-sankey-plot is designed to generate Sankey/alluvial plots from categorical sample annotation tables. Your request appears to be outside this scope. Please provide a sample annotation table with at least 2 categorical stage columns, or use a more appropriate tool for gene network visualization or pathway analysis."
Readability guidance: Sankey plots are recommended for fewer than 8 unique values per stage and fewer than 5 stages total. For larger inputs, filter or aggregate categories before plotting to ensure readable output.
Agent Response Contract
After a successful run, report to the caller:
Sankey plot generated successfully.
Stages plotted : <comma-separated stage column names>
Samples : <row count>
Output prefix : <output_prefix>
Outputs:
table/selected_annotations.csv
table/sankey_lodes.csv
plot/<output_prefix>.pdf
data/session_info.txt
Readability warnings (if any): <advisory messages or "none">
If the script exits with a non-zero status, surface the SKILL_* error code and message verbatim. Do not attempt to continue or retry silently.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need to run analysis | scripts/main.R |
Execute: Rscript scripts/main.R --input_file ... --output_dir ... |
| Need algorithm details | references/algorithm.md |
Alluvial transformation logic, assumptions, and plotting choices |
| Encounter errors | references/troubleshooting.md |
Common errors and solutions |
| Need CLI examples | references/cli-guide.md |
Detailed CLI examples |
| Need test data | tests/data/ |
Sample annotation tables for smoke tests and regression checks |
What ships with it
11 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.
- eval_report_sample-group-sankey-plot_result.json 13 KB
- references/algorithm.md 2.0 KB
- references/cli-guide.md 1.8 KB
- references/troubleshooting.md 2.3 KB
- scripts/functions.R 3.5 KB
- scripts/install_dependencies.R 1.1 KB
- scripts/main.R 4.9 KB
- scripts/run_analysis.R 2.7 KB
- scripts/utils.R 3.3 KB
- tests/data/sample_annotations.csv 130 B
- tests/run_smoke_test.R 1.4 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.
- 11d ago First seen · 262 lines · 64 tokens per session scan A 3a341a0a04f7
sample-group-sankey-plot is a skill published in the GitHub repository aipoch/medical-research-skills (1,855 stars, last pushed 1mo ago), licensed MIT. It adds 64 tokens to every session and 2,318 once invoked, about $0.0003 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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