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-perturb-prepnpx skills add TianGzlab/OmicsClaw --skill sc-perturb-prepgit 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-prep)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-perturb-prep"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-perturb-prep.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 | $0.00085 | $0.01759 |
| Opus 5 | $0.00043 | $0.00879 |
| Sonnet 5 | $0.00017 | $0.00352 |
| Haiku 4.5 | $0.00009 | $0.00176 |
Grade A, and why
sc-perturb-prep 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 — 124 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-perturb-prep
When to use
The user has Perturb-seq expression data (10x h5 / matrix dir / h5ad) and an upstream barcode-to-sgRNA mapping table (TSV / CSV from demultiplex / cellranger / cellbender output) and needs them merged into a single AnnData with:
obs[--pert-key](defaultperturbation) — canonical perturbation labelobs[--sgrna-key](defaultsgRNA) — guide identifierobs[--target-key](defaulttarget_gene) — inferred target geneobs["assignment_status"]—single_guide/multi_guide/unassignedobs["n_sgrnas"]— count per cell
Single backend: mapping_tsv. Then chain to sc-perturb for Mixscape
classification. This skill does NOT infer guide identities from FASTQ
— bring an upstream assignment table.
Inputs & Outputs
Inputs
- Input kinds:
file,directory - Modalities: scrna
- File types:
.h5ad,.h5,.loom,.tsv,.csv
Outputs
tables/assignment_status_counts.csvtables/cell_metadata.csvtables/dropped_multi_guide_cells.csvtables/feature_type_summary.csvtables/perturbation_assignments.csvtables/perturbation_counts.csvfigures/perturbation_counts.pnganalysis_summary.txtprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:perturbation,sgRNA,target_gene,assignment_status,n_sgrnas
Flow
- Load expression input via
smart_load; load mapping viaload_sgrna_mapping(auto-detect--sepif unset). - Strip non-gene features from
var(e.g., 10x guide / antibody capture rows). - Collapse mapping rows per cell: tag
single_guide/multi_guide/unassignedbased on row count. - Drop
multi_guidecells unless--keep-multi-guideis set. - Match each sgRNA against
--control-patterns(,-separated, includes default NT-style patterns); rewrite matches to--control-label(defaultNT). - Infer target gene from sgRNA ID via
--delimiter+--gene-position, OR use--target-columnfrom the mapping if provided. - Save standardised AnnData, 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 · 124 lines · 85 tokens per session scan A a7a44880d343
sc-perturb-prep is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 85 tokens to every session and 1,759 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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