A command for finding biological pathways associated with a ranked list of genes or a selected list of differentially expressed genes.

Use it for GSEA, which tests a full gene ranking, or ORA, which tests a selected gene list against a defined background. It reports false-discovery rates and leading-edge genes.

It helps interpret gene-level results by showing whether groups of genes linked to known biological processes appear more often than expected.

run-gsea — Command for Claude Code by zamushwani/biomedical-ai-skills

Install

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.

Clone the repo

git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/run-gsea/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/run-gsea)

Your own site

<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/run-gsea"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/run-gsea/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.

Your own site · 80×15

<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/run-gsea"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/run-gsea.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.

When invoked 300 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00000	$0.00300
Opus 5.5	$0.00000	$0.00120
Sonnet 5.5	$0.00000	$0.00060
Haiku 4.5	$0.00000	$0.00030

Measured 2mo ago against content hash 68264d72af46, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

run-gsea 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 2mo 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.

.claude/commands/run-gsea.md · 24 lines

What it actually says

Run pathway enrichment on $0 against the $1 collection (default: MSigDB Hallmark).

Follow the cancer-multiomics skill. Decide the method first:

ranked list, all genes    -> GSEA (fgsea). Uses the whole ranking.
a cut list of DEGs        -> ORA (enrichGO/enrichKEGG). Needs a background.

The parts that are usually got wrong:

Rank by the test statistic or shrunk LFC, not by p-value. A p-value is unsigned, so ranking by it puts strong up- and down-regulated genes at the same end.
ORA needs an explicit universe — the genes you actually tested, not every gene in the genome. The wrong background inflates every p-value.
Do not mix ID types. Convert once, and report how many genes failed to map rather than letting them vanish silently.
Report the FDR and the leading-edge genes, not just pathway names.

If $0 is empty, ask for the DE result file first.

Changes

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.

2mo ago First seen · 24 lines · 0 tokens per session scan A 68264d72af46

Subscribe to this mod's changes

run-gsea is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 300 tokens. 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 2026-08-31.

DESeq2 Scientific ai-agent ai-skills bioinformatics cancer-genomics cancer-research

run-gsea next to 6 commands from other repositories
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