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 sc-cytotracegit 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/sc-cytotrace)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-cytotrace"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-cytotrace/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/tiangzlab/omicsclaw/sc-cytotrace"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-cytotrace.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Rogue Agent · line 3 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
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 | $0.00063 | $0.01364 |
| Opus 5 | $0.00032 | $0.00682 |
| Sonnet 5 | $0.00013 | $0.00273 |
| Haiku 4.5 | $0.00006 | $0.00136 |
Grade A, and why
sc-cytotrace 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 — 114 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-cytotrace
When to use
The user has a normalised (or raw-count) scRNA AnnData and wants a
single per-cell differentiation potency score (0 = differentiated,
1 = stem/totipotent), plus a 6-bin categorical label
(Differentiated, Mostly Differentiated, ..., Totipotent). The
implementation uses the CytoTRACE-simple proxy: gene-expression
complexity (number of genes detected per cell), KNN-smoothed and rank-
normalised. Single backend: cytotrace_simple.
Output goes into obs["cytotrace_score"], obs["cytotrace_potency"],
obs["cytotrace_gene_count"]. For trajectory ordering use
sc-pseudotime; for cell-type labels use sc-cell-annotation.
Inputs & Outputs
Inputs
- Modalities: scrna
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present)
Outputs
tables/cell_metadata.csvtables/cytotrace_embedding.csvtables/cytotrace_scores.csvfigures/potency_composition.pngfigures/potency_umap.pngfigures/r_cell_density.pngfigures/r_cytotrace_boxplot.pngfigures/r_embedding_discrete.pngfigures/r_embedding_feature.pngfigures/score_distribution.pnganalysis_summary.txtprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:cytotrace_score,cytotrace_potency,cytotrace_gene_count
Flow
- Load AnnData; preflight requires
.Xto benormalized_expressionORraw_counts(matrix-contract check). - Compute per-cell gene-count complexity (number of detected genes).
- Rank-normalise gene counts; KNN-smooth across
--n-neighborsneighbours. - Min-max rescale to
[0, 1]→cytotrace_score. - Bin score into 6 potency categories; record counts per category.
- Detect degenerate output (≤ 1 unique category) → write
result.json["suggested_actions"]; do NOT raise. - Render figures, save tables,
processed.h5ad,report.md,result.json.
What ships with it
7 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.
- 8d ago First seen · 114 lines · 63 tokens per session scan A b1227075829c
sc-cytotrace is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 63 tokens to every session and 1,364 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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