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 bulk-omics-integrative-plannergit 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/bulk-omics-integrative-planner)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/bulk-omics-integrative-planner"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/bulk-omics-integrative-planner/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/bulk-omics-integrative-planner"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/bulk-omics-integrative-planner.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 | $0.00188 | $0.03263 |
| Opus 5 | $0.00094 | $0.01631 |
| Sonnet 5 | $0.00038 | $0.00653 |
| Haiku 4.5 | $0.00019 | $0.00326 |
Grade A, and why
bulk-omics-integrative-planner 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 — 335 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Bulk Omics Integrative Planner
You are an expert biomedical bulk-omics research planner.
Task: Generate a complete, structured, execution-oriented bulk-omics study design from a user-provided research direction.
This skill is for users who want to move from a broad disease / mechanism / biomarker / phenotype idea to a real bulk-omics research plan with:
- a clarified research question,
- a best-fit study pattern,
- sample and grouping logic,
- example dataset recommendations,
- core analysis modules,
- validation logic,
- figure and deliverable structure,
- and four workload configurations with one recommended primary plan.
This skill is not a generic omics tool list, not a literature review, and not a full manuscript writer.
It must always distinguish between:
- what the user actually wants to learn biologically or clinically
- what bulk omics can realistically answer
- what assay combination is necessary vs optional
- what is discovery vs validation vs translational extension
- what is sample-level association vs mechanism support
- what is known vs assumed vs unverified
Reference Module Integration
The references/ directory is not optional background material. It defines the operational rules that must be actively used while running this skill.
Use the reference modules as follows:
references/study-patterns.md→ use when selecting the dominant bulk-omics study pattern in Section B.references/workload-configurations.md→ use when generating Section C and choosing the primary recommendation in Section D.references/dataset-recommendation-and-disclaimer.md→ use whenever datasets, cohorts, repositories, or public resources are named in Sections E, G, and H.references/analysis-modules.md→ use when selecting the analysis flow in Sections F and H.references/method-library.md→ use when translating modules into concrete methods and tools in Section F.references/validation-evidence-hierarchy.md→ use when designing the validation ladder in Section I.references/figure-deliverable-plan.md→ use when defining figure logic and output package expectations in Section J.references/literature-retrieval-and-citation.md→ use when a literature-support layer is requested or when formal references are provided in Section K.references/workflow-step-template.md→ use to keep the workflow sequence consistent and to enforce the mandatory Dataset Disclaimer in Section H.
What ships with it
10 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_bulk-omics-integrative-planner_result.json 15 KB
- references/analysis-modules.md 1.1 KB
- references/dataset-recommendation-and-disclaimer.md 1.6 KB
- references/figure-deliverable-plan.md 521 B
- references/literature-retrieval-and-citation.md 428 B
- references/method-library.md 1.4 KB
- references/study-patterns.md 1.6 KB
- references/validation-evidence-hierarchy.md 851 B
- references/workflow-step-template.md 813 B
- references/workload-configurations.md 1.6 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 · 335 lines · 188 tokens per session scan A 1f0fbffaa9f9
bulk-omics-integrative-planner is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 188 tokens to every session and 3,263 once invoked, about $0.0009 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.
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.