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-cnvnpx skills add TianGzlab/OmicsClaw --skill spatial-cnvgit 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-cnv)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-cnv"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-cnv.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 | $0.00093 | $0.01951 |
| Opus 5 | $0.00046 | $0.00975 |
| Sonnet 5 | $0.00019 | $0.00390 |
| Haiku 4.5 | $0.00009 | $0.00195 |
Grade A, and why
spatial-cnv 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 yesterday.
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 — 133 lines — stays where its author put it; the contents beside it link to each section on GitHub.
spatial-cnv
When to use
The user has a preprocessed spatial AnnData with gene-coordinate
metadata in var["chromosome"] / var["start"] / var["end"] and
wants per-spot copy-number variation inferred for tumour / normal
deconvolution. Two backends:
infercnvpy(default) — log-ratio sliding-window over chromosomes usinginfercnvpy. Tunables--window-size,--step,--infercnv-lfc-clip,--infercnv-chunksize,--infercnv-n-jobs.numbat— R-based, allele-aware clone deconvolution using phased SNP allele counts. Requiresobsm["allele_counts"]. Tunables--numbat-genome(hg19/hg38),--numbat-max-entropy,--numbat-min-llr,--numbat-min-cells,--numbat-ncores.
--reference-key <obs col> + --reference-cat <category> define
the normal-reference subset (strongly recommended).
Inputs & Outputs
Inputs
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present) - Expects
obsm:spatial,allele_counts
Outputs
tables/allele_counts.csvtables/cnv_bin_summary.csvtables/cnv_group_sizes.csvtables/cnv_run_summary.csvtables/cnv_scores.csvtables/cnv_spatial_points.csvtables/cnv_umap_points.csvtables/numbat_calls.csvtables/numbat_clone_post.csvtables/numbat_results.csvfigures/cnv_bin_summary.pngfigures/cnv_group_sizes.pngfigures/cnv_groups_umap.pngfigures/cnv_heatmap.pngfigures/cnv_score_distribution.pngfigures/cnv_spatial.pngfigures/cnv_umap.pngfigures/cnv_uncertainty_distribution.pngfigures/cnv_uncertainty_spatial.pngnumbat_input.h5adprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:cnv_score,cnv_leiden,numbat_p_cnv,numbat_clone,numbat_entropy;uns:numbat_calls,numbat_clone_post
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.
- yesterday First seen · 133 lines · 93 tokens per session scan A ada7cb51a38a
spatial-cnv is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 93 tokens to every session and 1,951 once invoked, about $0.0005 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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