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/umap-tsne-analysisWrote 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/umap-tsne-analysis)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/umap-tsne-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/umap-tsne-analysis/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/umap-tsne-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/umap-tsne-analysis.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 | $0.00068 | $0.02739 |
| Opus 5 | $0.00034 | $0.01370 |
| Sonnet 5 | $0.00014 | $0.00548 |
| Haiku 4.5 | $0.00007 | $0.00274 |
Grade A, and why
umap-tsne-analysis 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 9d 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 — 315 lines — stays where its author put it; the contents beside it link to each section on GitHub.
UMAP and t-SNE Analysis
Prerequisites
Run the following before the first analysis to install all required R packages:
Rscript scripts/install_dependencies.R
Alternative manual installation:
Rscript -e "install.packages(c('optparse','data.table','Rtsne','umap','ggplot2','vegan','R.utils'), repos='https://cloud.r-project.org')"
Note:
R.utilsis only required when--timeout > 0, but pre-installing it avoids environment drift across runs.testthatis installed byscripts/install_dependencies.Ras the development test dependency.
The skill cannot run until these packages are installed. In new or bare R environments, always run the prerequisite step first.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
Dimensionality reduction methods, assumptions, parameter interpretation |
| 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 |
| Need test data | tests/data/ |
Sample input files for testing |
Usage
Rscript scripts/main.R \
--input_file ./otu_table.csv \
--group_file ./group_info.csv \
--output_dir ./output/ \
--method both \
--seed 42
Arguments
| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-i |
--input_file |
character | required | Abundance / OTU matrix file |
-g |
--group_file |
character | required | Group information file |
-o |
--output_dir |
character | ./output/ |
Output directory |
-m |
--method |
character | both |
Method: tsne, umap, or both |
--sample_id_col |
character | first column | Sample ID column in group file | |
--group_col |
character | second column | Group column in group file | |
--perplexity |
numeric | 25 |
t-SNE perplexity | |
--theta |
numeric | 0.0 |
t-SNE theta | |
--pca |
logical | FALSE |
Whether to use PCA before t-SNE | |
--check_duplicates |
logical | FALSE |
Whether t-SNE should check duplicated rows | |
--normalize |
logical | TRUE |
Whether to normalize data before UMAP | |
--norm_method |
character | hellinger |
Normalization method for vegan::decostand() |
|
--n_neighbors |
integer | 10 |
UMAP neighborhood size | |
-s |
--seed |
integer | 42 |
Random seed for reproducibility |
-t |
--timeout |
integer | 0 |
Timeout in seconds; 0 disables timeout |
What ships with it
16 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.
- dependencies.lock.tsv 199 B
- eval_report_umap-tsne-analysis_result.json 13 KB
- references/algorithm.md 3.7 KB
- references/cli-guide.md 6.4 KB
- references/troubleshooting.md 4.8 KB
- scripts/dim_reduction_methods.R 2.2 KB
- scripts/functions.R 2.3 KB
- scripts/install_dependencies.R 2.7 KB
- scripts/main.R 5.7 KB
- scripts/run_analysis.R 2.0 KB
- scripts/utils.R 7.3 KB
- scripts/visualization.R 2.6 KB
- tests/data/group_info.csv 2.2 KB
- tests/data/otu_table.csv 853 KB
- tests/run_smoke_test.R 1.8 KB
- tests/testthat/test-core.R 2.5 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.
- 9d ago First seen · 315 lines · 68 tokens per session scan A ed77cd50292e
umap-tsne-analysis is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 68 tokens to every session and 2,739 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 2026-09-03.
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