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 AndyZhuang/Opentest --skill tooluniverse-spatial-transcriptomicsgit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote 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/andyzhuang/opentest/tooluniverse-spatial-transcriptomics)<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-spatial-transcriptomics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-spatial-transcriptomics/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/andyzhuang/opentest/tooluniverse-spatial-transcriptomics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-spatial-transcriptomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00122 | $0.05969 |
| Opus 5 | $0.00061 | $0.02985 |
| Sonnet 5 | $0.00024 | $0.01194 |
| Haiku 4.5 | $0.00012 | $0.00597 |
Grade A, and why
tooluniverse-spatial-transcriptomics 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 8d 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 — 789 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Spatial Transcriptomics Analysis
Comprehensive analysis of spatially-resolved transcriptomics data to understand gene expression patterns in tissue architecture context. Combines expression profiling with spatial coordinates to reveal tissue organization, cell-cell interactions, and spatially variable genes.
When to Use This Skill
Triggers:
- User has spatial transcriptomics data (Visium, MERFISH, seqFISH, etc.)
- Questions about tissue architecture or spatial organization
- Spatial gene expression pattern analysis
- Cell-cell proximity or neighborhood analysis requests
- Tumor microenvironment spatial structure questions
- Integration of spatial with single-cell data
- Spatial domain identification
- Tissue morphology correlation with expression
Example Questions This Skill Solves:
- "Analyze this 10x Visium dataset to identify spatial domains"
- "Which genes show spatially variable expression in this tissue?"
- "Map the tumor microenvironment spatial organization"
- "Find genes enriched at tissue boundaries"
- "Identify cell-cell interactions based on spatial proximity"
- "Integrate spatial transcriptomics with scRNA-seq annotations"
- "Characterize spatial gradients in gene expression"
- "Map ligand-receptor pairs in tissue context"
Core Capabilities
| Capability | Description |
|---|---|
| Data Import | 10x Visium, MERFISH, seqFISH, Slide-seq, STARmap, Xenium formats |
| Quality Control | Spot/cell QC, spatial alignment verification, tissue coverage |
| Normalization | Spatial-aware normalization accounting for tissue heterogeneity |
| Spatial Clustering | Identify spatial domains with similar expression profiles |
| Spatial Variable Genes | Find genes with non-random spatial patterns |
| Neighborhood Analysis | Cell-cell proximity, spatial neighborhoods, niche identification |
| Spatial Patterns | Gradients, boundaries, hotspots, expression waves |
| Integration | Merge with scRNA-seq for cell type mapping |
| Ligand-Receptor Spatial | Map cell communication in tissue context |
| Visualization | Spatial plots, heatmaps on tissue, 3D reconstruction |
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.
- 8d ago First seen · 789 lines · 122 tokens per session scan A b51e020deceb
tooluniverse-spatial-transcriptomics is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It adds 122 tokens to every session and 5,969 once invoked, about $0.0006 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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