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 deg-screening-analysisgit 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/deg-screening-analysis)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/deg-screening-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/deg-screening-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/deg-screening-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/deg-screening-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 | $0.00096 | $0.01975 |
| Opus 5 | $0.00048 | $0.00988 |
| Sonnet 5 | $0.00019 | $0.00395 |
| Haiku 4.5 | $0.00010 | $0.00198 |
Grade A, and why
deg-screening-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 13d 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 — 160 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Differential Expression Gene Screening Analysis (Volcano Plot & Clustered Heatmap)
When to Use
Use this skill when you need a reproducible two-group DEG workflow on a bulk expression matrix and want:
- a full differential expression table
- a filtered DEG table
- a volcano plot
- a clustered heatmap of top differential genes
Typical requests include:
- compare case vs control samples with limma
- screen upregulated and downregulated genes from a normalized expression matrix
- generate a DEG table with volcano and heatmap outputs from bulk transcriptome data
Out of Scope
Do not use this skill for:
- single-cell RNA-seq workflows
- multi-group contrasts or factorial designs
- count-model pipelines that require
DESeq2oredgeR - batch correction, covariate-adjusted models, or generalized design-matrix consulting
- non-expression omics data
If the request falls outside this scope, stop and hand off to a more appropriate analysis workflow instead of forcing the data through this skill.
Practical Caveats
Diffanalysis.csvcurrently exportsname,logFC,P.value, andP.adj.--p_typecontrols both DEG screening semantics and volcano plot significance semantics.plot/heatmap.pdfis generated only when at least two heatmap genes remain after ranking.- When the result is very sparse, prefer keeping tables and volcano output as the primary artifacts.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details or statistical assumptions | references/algorithm.md |
limma method, filtering logic, volcano/heatmap selection rules |
| Need to execute the workflow | scripts/main.R |
Get the exact CLI entry and runnable command |
| Encounter an error code or bad input format | references/troubleshooting.md |
Match SKILL_* errors to causes and fixes |
| Need more CLI examples | references/cli-guide.md |
See complete command examples for common use cases |
| Need a minimal runnable example | tests/data/ |
Use bundled test input files for validation |
What ships with it
13 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_deg-screening-analysis_result.json 15 KB
- references/algorithm.md 3.2 KB
- references/cli-guide.md 4.5 KB
- references/troubleshooting.md 3.6 KB
- scripts/diff_methods.R 875 B
- scripts/diff_visualization.R 4.9 KB
- scripts/functions.R 5.0 KB
- scripts/main.R 3.9 KB
- scripts/run_analysis.R 3.0 KB
- scripts/utils.R 6.7 KB
- tests/data/oa_exp.csv 998 KB
- tests/data/oa_group.csv 2.2 KB
- tests/run_tests.R 8.5 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.
- 13d ago First seen · 160 lines · 96 tokens per session scan A 6c396523fd87
deg-screening-analysis is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 96 tokens to every session and 1,975 once invoked, about $0.0005 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
statistical-modeling
Statistical modeling and machine learning for biomarker discovery, survival analysis, classification, regression, and model interpretation.
bulk-transcriptomics
Bulk RNA-seq and microarray differential expression analysis including method selection, batch correction, and complex experimental designs.
chromatin-regulation
Chromatin regulation analysis from called peaks and count matrices — differential binding, signal summarisation, peak annotation, and scATAC-seq.
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.