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 estimate-immune-score-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/estimate-immune-score-analysis)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/estimate-immune-score-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/estimate-immune-score-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/estimate-immune-score-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/estimate-immune-score-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 | $0.00090 | $0.02926 |
| Opus 5 | $0.00045 | $0.01463 |
| Sonnet 5 | $0.00018 | $0.00585 |
| Haiku 4.5 | $0.00009 | $0.00293 |
Grade A, and why
estimate-immune-score-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 — 291 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ESTIMATE Immune Score Analysis
When to Use
Use this skill when the user wants to:
- compute ESTIMATE-derived immune and stromal scores from a bulk expression matrix
- transform an expression matrix into
estimatepackage input files and score outputs - generate an ESTIMATE score heatmap across samples
- compare ESTIMATE scores across sample groups when a sample group file is available
- create a reproducible CLI-backed ESTIMATE workflow with structured output records
Typical request patterns:
- "Run ESTIMATE immune score analysis on this expression matrix"
- "Calculate ImmuneScore and StromalScore from my bulk RNA-seq data"
- "Generate ESTIMATE scores and save a sample-level result table"
Execution Model
This is a CLI-backed analysis skill.
- Use
SKILL.mdto confirm that the task is ESTIMATE score generation from bulk expression data. - Use
scripts/main.Rfor the real execution. - Provide one expression matrix file with genes in the first column and samples in the remaining columns.
- Optionally provide a sample group file to generate ESTIMATE score boxplots and a significance summary table.
- The workflow always generates an ESTIMATE score heatmap from the computed score table.
- Read reference files only when you need algorithm details, troubleshooting, or baseline execution notes.
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
Understand the ESTIMATE scoring workflow and result interpretation |
| Need to run the skill | 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 real-data baseline record | references/cli-guide.md |
Copy commands and review the recorded execution template |
| Need sample input files | tests/data/ |
Use the bundled demo expression matrix |
When Not to Use
- Immune cell fraction estimation: use a CIBERSORT-like deconvolution workflow instead
- Differential testing between biological groups: use a differential analysis skill instead
- Single-cell analysis: use a single-cell-specific workflow
- Clinical diagnosis or treatment decision support: do not use this skill
What ships with it
15 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_estimate-immune-score-analysis_result.json 13 KB
- references/algorithm.md 2.5 KB
- references/cli-guide.md 6.1 KB
- references/troubleshooting.md 4.2 KB
- scripts/cli_options.R 3.6 KB
- scripts/functions.R 5.5 KB
- scripts/io.R 2.4 KB
- scripts/main.R 3.8 KB
- scripts/recording.R 4.0 KB
- scripts/run_analysis.R 2.6 KB
- scripts/utils.R 4.8 KB
- scripts/visualization.R 6.6 KB
- tests/data/expression_matrix.csv 39 KB
- tests/data/group_info.csv 202 B
- tests/run_tests.R 868 B
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 · 291 lines · 90 tokens per session scan A 3eb2761d3966
estimate-immune-score-analysis is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 90 tokens to every session and 2,926 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.