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 gsva-analysis-and-visualizationgit 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/gsva-analysis-and-visualization)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/gsva-analysis-and-visualization"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/gsva-analysis-and-visualization/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/gsva-analysis-and-visualization"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/gsva-analysis-and-visualization.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 | $0.00088 | $0.04065 |
| Opus 5 | $0.00044 | $0.02032 |
| Sonnet 5 | $0.00018 | $0.00813 |
| Haiku 4.5 | $0.00009 | $0.00407 |
Grade A, and why
gsva-analysis-and-visualization 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 — 343 lines — stays where its author put it; the contents beside it link to each section on GitHub.
GSVA Analysis And Visualization
When to Use
Use this skill when the user wants one of the following:
- Pathway-level GSVA or ssGSEA analysis from a bulk expression matrix plus a sample group file
- Case-vs-control or treatment-vs-control pathway enrichment comparison using GSVA plus limma
- KEGG or MSigDB pathway analysis for bulk RNA-seq or microarray-like expression data
- Heatmap generation from an existing
data/GSVA_list.rdaresult object - A reproducible CLI-backed GSVA workflow with saved tables, an
.rdaobject, and a PDF heatmap
Typical request patterns:
- "Run GSVA on my bulk RNA-seq matrix and compare case vs control"
- "Use ssGSEA to score pathways and save the pathway differential results"
- "Generate a KEGG pathway heatmap from my saved GSVA result"
- "Do pathway enrichment with GSVA for these grouped bulk samples"
Execution Model
This is a hybrid skill.
- Use
SKILL.mdto verify that the request is in scope. - Use
scripts/main.Rfor real execution. - Use
--mode analyzeto compute pathway scores and differential results. - Use
--mode visualizeto reuse an existingdata/GSVA_list.rdaand generate a heatmap. In visualize mode,GSVA_list.rdamust exist inoutput_dir/data/; runanalyzeorfullmode first if it is missing (SKILL_FILE_NOT_FOUNDwill be raised otherwise). - Use
--mode fullto run analysis and visualization in one pass. - Read reference files only when you need algorithm details, troubleshooting, or additional CLI examples.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
Understand GSVA, limma, and heatmap generation logic |
| Need to run analysis or plotting | scripts/main.R |
Execute the CLI entry point |
| Encounter errors | references/troubleshooting.md |
Find standard error codes and fixes |
| Need more CLI examples or the baseline execution record | references/cli-guide.md |
Copy ready-to-run commands and review the recorded test run |
| Need sample input files | tests/data/ |
Use the bundled demo matrix and group file |
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.
- eval_report_gsva-analysis-and-visualization_result.json 16 KB
- references/algorithm.md 2.5 KB
- references/cli-guide.md 5.8 KB
- references/troubleshooting.md 2.5 KB
- scripts/cli_options.R 6.9 KB
- scripts/functions.R 4.4 KB
- scripts/io.R 3.4 KB
- scripts/main.R 4.6 KB
- scripts/plot_helpers.R 2.7 KB
- scripts/recording.R 3.4 KB
- scripts/run_analysis.R 2.3 KB
- scripts/utils.R 2.8 KB
- scripts/visualization.R 3.0 KB
- tests/data/expr_matrix.csv 24935 KB
- tests/data/group.csv 2.7 KB
- tests/run_tests.R 2.1 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 · 343 lines · 88 tokens per session scan A 5fc350c43e98
gsva-analysis-and-visualization is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 88 tokens to every session and 4,065 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.
Other skills, from other repositories
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chromatin-regulation
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bulk-transcriptomics
Bulk RNA-seq and microarray differential expression analysis including method selection, batch correction, and complex experimental designs.
spatial-omics
Spatial transcriptomics and spatial proteomics analysis covering technology-specific workflows, spatial statistics, deconvolution, and niche analysis.
atac-seq-bam-read-alignment-processing
Use when when you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites, peaks, regulatory regions) to detect transcription factor occupancy footprints or compare chromatin accessibility between bound and unbound.
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.