What is bioconductor-spatialexperiment?

An R data structure for storing results from spatial omics experiments, which measure molecular activity together with physical tissue locations. It supports both spot-based and molecule-based platforms and extends Bioconductor's single-cell data structure.

Use it to store and retrieve expression measurements, coordinates, and metadata from spatial transcriptomics experiments.

It keeps expression data, spatial coordinates, and related information together in a standard format. This makes spatial experiment data easier for other analysis tools to use.

bioconductor-spatialexperiment — Skill for Claude Code by bioMate-AI

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 spatialexperiment

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment/github.svg)](https://agentmods.dev/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment)

Your own site

<a href="https://agentmods.dev/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment"><img src="https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment/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/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment"><img src="https://agentmods.dev/badge/skills/biomate-ai/biomate-bioconductor-kb/spatialexperiment.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,275 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.

Model	Per session	Once invoked
Fable 5.1	$0.00047	$0.01275
Opus 5.5	$0.00019	$0.00510
Sonnet 5.5	$0.00009	$0.00255
Haiku 4.5	$0.00005	$0.00128

Measured 2mo ago against content hash b3246c68a358, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

bioconductor-spatialexperiment 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.

skills/transcriptomics/spatialexperiment/SKILL.md · 71 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.

2mo ago First seen · 71 lines · 47 tokens per session scan A b3246c68a358

Subscribe to this mod's changes

bioconductor-spatialexperiment is a skill published in the GitHub repository bioMate-AI/biomate-bioconductor-kb (792 stars, last pushed 4mo ago), with no licence file. It adds 47 tokens to every session and 1,275 once invoked, about $0.0002 per session on Opus 5.5. 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.

Data and AI Scientific

bioconductor-spatialexperiment next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
bioconductor-spatialexperimentbioMate-AI/biomate-bioconductor-kb	Skill	792	4mo ago	none	A	47	Claude Code
arboretoK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	55	Claude Code, Codex
deepspot-mK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	70	Claude Code
torchdrugK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	64	Claude Code
pyhealthK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	84	Claude Code, Codex
nemo-mbridge-perf-expert-parallel-overlapNVIDIA/skills	Skill	3.9k	yesterday	Apache-2.0	A	56	Claude Code
ml-training-recipesOrchestra-Research/AI-Research-SKILLs	Skill	14k	27d ago	MIT	A	88	Claude Code