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/cerna-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/cerna-analysis)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/cerna-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/cerna-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/cerna-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/cerna-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 | $0.02448 |
| Opus 5 | $0.00034 | $0.01224 |
| Sonnet 5 | $0.00014 | $0.00490 |
| Haiku 4.5 | $0.00007 | $0.00245 |
Grade A, and why
cerna-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 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 — 218 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ceRNA Analysis
When to Use
Use this skill when you need to construct a ceRNA regulatory network from a known key-gene list using the bundled miRNA-mRNA and miRNA-lncRNA reference tables.
Use it for:
- Building a ceRNA network from one gene list and exporting flat CSV plus PDF outputs
- Comparing supported miRNA source modes such as
combined,starbase, or pairwise overlaps - Re-running the same local workflow with different lncRNA strictness, layout, or plotting parameters
Do not use it for:
- Differential expression, single-cell, enrichment, or survival analysis
- Workflows that do not start from a key gene list
- Cases where you want a miRNA-mRNA-only graph without a retained lncRNA ceRNA layer
Input Validation
This skill accepts:
- A key gene list as a plain-text file (one gene symbol per line) or as a comma-separated string on the CLI
- Optional parameter overrides for dataset mode, lncRNA strictness, layout, colors, and timeout
If the user's request does not involve building a ceRNA regulatory network from a key gene list — for example, asking to run differential expression, enrichment analysis, single-cell workflows, or survival analysis — do not proceed with the workflow. Instead respond:
"ceRNA Analysis is designed to construct a ceRNA regulatory network from a key gene list using bundled miRNA-mRNA and miRNA-lncRNA reference databases. Your request appears to be outside this scope. Please provide a key gene list and specify a supported miRNA dataset mode, or use a more appropriate skill for differential expression, enrichment analysis, or single-cell workflows."
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
ceRNA construction logic, dataset combinations, filtering rules. Includes worked examples of pairwise intersection network size vs combined mode. |
| Need to run analysis | scripts/main.R |
Execute: Rscript scripts/main.R --key_genes ... --output_dir .... Note: --help requires igraph to be installed. |
| Encounter errors | references/troubleshooting.md |
Common errors and solutions |
| Need CLI examples | references/cli-guide.md |
Detailed local run examples with measured outputs |
| Need test data | tests/data/ |
Sample key-gene input for testing |
What ships with it
22 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_cerna-analysis_result.json 18 KB
- references/algorithm.md 2.3 KB
- references/cli-guide.md 7.4 KB
- references/database/miRDB_miRNA_mRNA.csv 49178 KB
- references/database/miRNA_mRNA.csv 579 KB
- references/database/miRTarbase_miRNA_mRNA.csv 11446 KB
- references/database/starbase_miRNA_lncRNA_High.csv 102 KB
- references/database/starbase_miRNA_lncRNA_Low.csv 326 KB
- references/database/starbase_miRNA_lncRNA_Median.csv 163 KB
- references/database/starbase_miRNA_mRNA.csv 12379 KB
- references/troubleshooting.md 3.6 KB
- scripts/functions.R 2.4 KB
- scripts/io.R 3.1 KB
- scripts/main.R 5.8 KB
- scripts/plot_functions.R 3.0 KB
- scripts/run_analysis.R 1.7 KB
- scripts/utils.R 3.9 KB
- scripts/validation.R 2.5 KB
- tests/data/gene.txt 18 B
- tests/run_tests.R 308 B
- tests/testthat/helper-load-scripts.R 925 B
- tests/testthat/test-standardization.R 6.0 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 · 218 lines · 68 tokens per session scan A 38427e214218
cerna-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 2,448 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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Use when after identifying a set of differentially accessible peaks (via tl.difftest or equivalent), when you need to infer which transcription factors may regulate the observed chromatin state changes.
motif-peak-overlap-matching
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