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 TianGzlab/OmicsClaw --skill spatial-enrichmentgit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote 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/tiangzlab/omicsclaw/spatial-enrichment)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-enrichment"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-enrichment.svg" alt="Measured on agentmods" 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 | $0.00069 | $0.01876 |
| Opus 5 | $0.00034 | $0.00938 |
| Sonnet 5 | $0.00014 | $0.00375 |
| Haiku 4.5 | $0.00007 | $0.00188 |
Grade A, and why
spatial-enrichment 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 3d 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 — 139 lines — stays where its author put it; the contents beside it link to each section on GitHub.
spatial-enrichment
When to use
The user has a preprocessed spatial AnnData with cluster labels in
obs[groupby] (default leiden) and wants pathway / gene-set
enrichment per cluster. Three backends:
enrichr(default) — over-representation against an Enrichr hosted gene-set library. Tunables--enrichr-padj-cutoff,--enrichr-log2fc-cutoff,--enrichr-max-genes.gsea— preranked GSEA. Tunables--gsea-min-size,--gsea-max-size,--gsea-permutation-num,--gsea-weight,--gsea-threads,--gsea-seed.ssgsea— single-sample GSEA per cell, scores written back toobs[...]. Tunables--ssgsea-min-size,--ssgsea-max-size,--ssgsea-weight.
--gene-set selects a hosted library (e.g. MSigDB_Hallmark_2020);
--gene-set-file accepts a custom GMT. Species: human (default)
or mouse. For non-spatial enrichment use sc-enrichment.
Inputs & Outputs
Inputs
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present) - Expects
obsm:spatial
Outputs
tables/enrichment_group_metrics.csvtables/enrichment_results.csvtables/enrichment_run_summary.csvtables/enrichment_significant.csvtables/enrichment_spatial_points.csvtables/enrichment_term_group_scores.csvtables/enrichment_umap_points.csvtables/ranked_markers.csvtables/top_enriched_terms.csvfigures/enrichment_barplot.pngfigures/enrichment_dotplot.pngfigures/enrichment_group_metrics.pngfigures/enrichment_group_spatial_context.pngfigures/enrichment_group_top_stat_spatial.pngfigures/enrichment_group_top_stat_umap.pngfigures/enrichment_pvalue_distribution.pngfigures/enrichment_score_distribution.pngfigures/enrichment_score_violin.pngfigures/enrichment_spatial_scores.pngfigures/top_enriched_terms.pngprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsuns:enrichment_results,{method}_results,enrichr_results,gsea_results,ssgsea_results,enrichment_score_columns
What ships with it
8 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.
- 3d ago First seen · 139 lines · 69 tokens per session scan A 6b6ac9c8cc52
spatial-enrichment is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 69 tokens to every session and 1,876 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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