bioconductor-gsva

bioconductor-gsva is a skill for Claude Code from bioMate-AI/biomate-bioconductor-kb. It costs 54 tokens per session (1,343 once invoked), scanned A, original, no licence file.

A method for measuring how the activity of predefined gene groups varies across samples in an expression dataset. Gene Set Variation Analysis, or GSVA, converts gene-level measurements into scores for gene sets.

In plain words
What is it for?
Use it to calculate gene-set activity scores and study how biological pathways vary across samples.
Why use it?
It helps reveal pathway-level differences when individual genes are noisy or difficult to interpret. The method works without preassigning sample groups.

Skill for Claude Code

Written for Claude Code: user-invocable in frontmatter.

Good fit Use it to calculate gene-set activity scores and study how biological pathways vary across samples.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/biomate-ai/biomate-bioconductor-kb/gsva
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.

Any agent
npx skills add bioMate-AI/biomate-bioconductor-kb --skill gsva
Clone the repo
git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb

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.

agentmods badge for bioconductor-gsva

README.md
[![agentmods](https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/gsva/github.svg)](https://agentmods.dev/skills/biomate-ai/biomate-bioconductor-kb/gsva)
Your own site
<a href="https://agentmods.dev/skills/biomate-ai/biomate-bioconductor-kb/gsva"><img src="https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/gsva/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.

agentmods 80×15 button for bioconductor-gsva

Your own site · 80×15
<a href="https://agentmods.dev/skills/biomate-ai/biomate-bioconductor-kb/gsva"><img src="https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/gsva.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 54 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,343 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 unknown 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00054 $0.01343
Opus 5 $0.00027 $0.00672
Sonnet 5 $0.00011 $0.00269
Haiku 4.5 $0.00005 $0.00134

Measured 9d ago against content hash 8db21f7350b3, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

bioconductor-gsva 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.

skills/transcriptomics/gsva/SKILL.md · 72 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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.

  1. 9d ago First seen · 72 lines · 54 tokens per session scan A 8db21f7350b3

Subscribe to this mod's changes

bioconductor-gsva is a skill published in the GitHub repository bioMate-AI/biomate-bioconductor-kb (808 stars, last pushed 2mo ago), with no licence file. It adds 54 tokens to every session and 1,343 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 2026-09-03.

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