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/sc-perturbnpx skills add TianGzlab/OmicsClaw --skill sc-perturbgit 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-perturb)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-perturb"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-perturb.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 | $0.00084 | $0.01579 |
| Opus 5 | $0.00042 | $0.00790 |
| Sonnet 5 | $0.00017 | $0.00316 |
| Haiku 4.5 | $0.00008 | $0.00158 |
Grade A, and why
sc-perturb 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 — 120 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-perturb
When to use
The user has a scRNA AnnData from a CRISPR perturbation screen
(Perturb-seq style) where each cell already carries a perturbation
label in obs[--pert-key] plus a control category. The skill runs
pertpy's Mixscape workflow to:
- Compute a per-cell perturbation signature (subtracts the matched
control profile in
obsm["X_pca"]). - Classify cells as
KO/NT/NP(non-perturbed / escapers). - Report responder vs non-responder structure per perturbation +
--split-bygroup.
Single backend: mixscape (forward-compatible CLI choice). For
attaching guide labels to expression first, use sc-perturb-prep. For
predicting perturbation effects on unperturbed data, use
sc-in-silico-perturbation.
Inputs & Outputs
Inputs
- Modalities: scrna
- File types:
.h5ad
Outputs
tables/cell_metadata.csvtables/cell_type_counts.csvtables/mixscape_cell_classes.csvtables/mixscape_class_counts.csvtables/mixscape_global_class_counts.csvtables/mixscape_global_classes.csvfigures/mixscape_global_classes.pngfigures/r_perturbation_barplot.pnganalysis_summary.txtprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:mixscape_class,mixscape_class_global,mixscape_class_p_<lower(perturbation_type)>
Flow
- Load AnnData (
--input) or generate demo Perturb-seq data. - Validate
obs[--pert-key]exists and--controlis a real category in that column. - Warn-and-disable
--split-byif the column is absent (does NOT raise). - Compute
obsm["X_pca"]if missing (auto-runssc.pp.pca). - Run
pertpy.tools.Mixscape(perturbation signature + KO/NT/NP classification). - Detect degenerate output (e.g., everything classified as
NP) and write troubleshooting hints. - Save
processed.h5ad, tables, figure,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.
- 2d ago First seen · 120 lines · 84 tokens per session scan A 24d9ac4d3868
sc-perturb is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 84 tokens to every session and 1,579 once invoked, about $0.0004 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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