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 genomics-epigenomicsgit 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/genomics-epigenomics)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-epigenomics"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-epigenomics.svg" alt="Measured on agentmods" 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 | $0.00079 | $0.01160 |
| Opus 5 | $0.00039 | $0.00580 |
| Sonnet 5 | $0.00016 | $0.00232 |
| Haiku 4.5 | $0.00008 | $0.00116 |
Grade A, and why
genomics-epigenomics 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 — 90 lines — stays where its author put it; the contents beside it link to each section on GitHub.
genomics-epigenomics
When to use
The user has a peak file (BED, narrowPeak, or broadPeak) from
ATAC-seq, ChIP-seq, or CUT&Tag and wants peak summary statistics:
total peak count, median / mean width, per-chromosome distribution,
optional score column statistics. The script consumes peak files —
it does NOT call peaks from BAM. --method (macs2 / macs3 /
homer / genrich) and --assay (chip-seq / atac-seq /
cut-tag) are recorded as metadata only.
For single-cell ATAC processing use scatac-preprocessing.
Inputs & Outputs
Inputs
- Modalities: atac-seq, chip-seq
- File types:
.bed,.narrowpeak,.csv
Outputs
tables/peaks_per_chromosome.csvtables/peaks_summary.csvreport.mdresult.json
Flow
- Load peak file (
--input <peaks.bed|narrowPeak>) or generate a demo atoutput_dir/demo_peaks.narrowPeak(genomics_epigenomics.py:211). - Parse coordinates; compute per-peak width.
- Aggregate per-chromosome counts; per-
--assayexpected-width range is added to the report (genomics_epigenomics.py:172-178). - Write
tables/peaks_summary.csv(genomics_epigenomics.py:352) +tables/peaks_per_chromosome.csv(:360) +report.md+result.json(:366).
Gotchas
- No peak caller is invoked. This skill summarises an existing BED/narrowPeak file — it does NOT run MACS / Genrich. Run them upstream and feed the output here.
--methodis metadata-only;--assaychanges the report.--methodis recorded inresult.jsononly.--assaycontrols the per-assay expected-peak-width range injected into the summary (genomics_epigenomics.py:172-178) —chip-seqreports 200-2000 bp,atac-seq150-500 bp,cut-tag150-300 bp. Peak parsing itself is identical across assays.--inputREQUIRED unless--demo.genomics_epigenomics.py:334raisesValueError("--input required when not using --demo"); non-existent paths raiseFileNotFoundErrorat:337.- 3-column BED has no score column. Without a score (col 5 in BED6 / narrowPeak), the summary statistics for "score" are NaN. Pre-convert to narrowPeak or BED6 for score-aware stats. Note: broadPeak's "signalValue" (col 7) and qValue (col 9) are NOT read — the parser only handles up to BED6 plus the narrowPeak 10-col extension.
- Coordinate convention is 0-based half-open (BED). Width =
end - start. If your input uses 1-based closed coordinates, widths are off-by-one. - Demo BED has 500 fixed-pattern peaks. Useful for orchestrator smoke tests; not biologically meaningful.
What ships with it
5 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 · 90 lines · 79 tokens per session scan A 05e4e5647ec3
genomics-epigenomics is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 79 tokens to every session and 1,160 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 2026-08-30.
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