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 agentmods add skills/tiangzlab/omicsclaw/spatial-transcriptomicsnpx skills add TianGzlab/OmicsClaw --skill spatial-transcriptomicsgit clone --depth 1 https://github.com/TianGzlab/OmicsClawWhat 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 | $0.00006 | $0.03204 |
| Opus 5 | $0.00003 | $0.01602 |
| Sonnet 5 | $0.00001 | $0.00641 |
| Haiku 4.5 | $0.00001 | $0.00320 |
Grade A, and why
Spatial Transcriptomics Visium 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 2d 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 — 257 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Spatial Transcriptomics Visium Analysis
When to Use This Skill
- You have 10x Visium spatial gene expression data (with or without H&E image)
- You want to identify spatially variable genes across a tissue section
- You want to discover spatial tissue domains via clustering
- You want to quantify neighborhood enrichment between cell clusters
- You want to analyze co-occurrence patterns of cell types across distances
- Input is Space Ranger output,
.h5ad, or.h5file
Not for: Single-molecule FISH (MERFISH/Xenium), Slide-seq, or single-cell RNA-seq without spatial coordinates. For scRNA-seq, use scrnaseq-scanpy-core-analysis.
Installation
pip install squidpy scanpy anndata scikit-misc plotnine plotnine-prism seaborn matplotlib numpy pandas scikit-learn
| Package | Version | License | Commercial Use | Installation |
|---|---|---|---|---|
| squidpy | ≥1.4 | BSD-3-Clause | ✅ Permitted | pip install squidpy |
| scanpy | ≥1.9 | BSD-3-Clause | ✅ Permitted | pip install scanpy |
| anndata | ≥0.8 | BSD-3-Clause | ✅ Permitted | pip install anndata |
| plotnine | ≥0.12 | MIT | ✅ Permitted | pip install plotnine |
| plotnine-prism | ≥0.2 | MIT | ✅ Permitted | pip install plotnine-prism |
| seaborn | ≥0.11 | BSD-3-Clause | ✅ Permitted | pip install seaborn |
| matplotlib | ≥3.5 | PSF | ✅ Permitted | pip install matplotlib |
| scikit-learn | ≥1.0 | BSD-3-Clause | ✅ Permitted | pip install scikit-learn |
| scikit-misc | ≥0.1 | BSD-3-Clause | ✅ Permitted | pip install scikit-misc |
| numpy | ≥1.21 | BSD-3-Clause | ✅ Permitted | pip install numpy |
| pandas | ≥1.3 | BSD-3-Clause | ✅ Permitted | pip install pandas |
License Compliance: All packages use permissive licenses (BSD, MIT, PSF) that permit commercial use in AI agent applications.
Inputs
| Input | Format | Description |
|---|---|---|
| Visium data | .h5ad, .h5, or Space Ranger directory |
Gene expression + spatial coordinates |
| H&E image | Embedded in above | Tissue histology (optional, enhances spatial plots) |
What ships with it
5 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.
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.
- 2d ago First seen · 257 lines · 6 tokens per session scan A 548fe8b3c528
Spatial Transcriptomics Visium Analysis is a skill published in the GitHub repository TianGzlab/OmicsClaw (159 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 6 tokens to every session and 3,204 once invoked, about $0.0000 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.
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