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 zongtingwei/Bioclaw_Skills_Hub --skill chip-seqgit clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_HubWrote 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/zongtingwei/bioclaw_skills_hub/chip-seq)<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/chip-seq"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/chip-seq/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/zongtingwei/bioclaw_skills_hub/chip-seq"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/chip-seq.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00032 | $0.01281 |
| Opus 5 | $0.00016 | $0.00641 |
| Sonnet 5 | $0.00006 | $0.00256 |
| Haiku 4.5 | $0.00003 | $0.00128 |
Grade A, and why
chip-seq 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 12d 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 — 171 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ChIP Seq
Version Compatibility
Reference examples assume:
macs33.0+samtools1.18+deepTools3.5+
Before using commands, verify the installed environment:
- CLI:
macs3 --version,samtools --version,bamCoverage --version - If flags differ, inspect
--helpand adapt rather than forcing the example unchanged.
Overview
Use this skill for:
- narrow or broad peak calling
- input-normalized signal tracks
- peak annotation
- motif follow-up
- differential binding review when replicates exist
When To Use This Skill
- the user has aligned ChIP and optional input BAM files
- the deliverable includes peaks, browser tracks, or motif results
- the assay is TF ChIP or histone-mark ChIP and needs standard peak-centric processing
Quick Route
- TF or narrow marks: use narrow peak mode first.
- H3K27me3, H3K36me3, or other broad marks: use
--broad. - Paired-end BAM: prefer
-f BAMPE. - No input control: still possible, but report the limitation explicitly.
Progressive Disclosure
- Read technical_reference.md for QC gates, narrow-versus-broad logic, and replicate handling.
- Read commands_and_thresholds.md for MACS3 commands, parameter defaults, and output file conventions.
Prerequisites
| Requirement | Narrow TF-style | Broad histone-style |
|---|---|---|
| usable uniquely mapped reads | >= 10M |
>= 20M |
| matched input recommended | yes | yes |
| biological replicates recommended | >= 2 |
>= 2 |
Expected Inputs
chip.baminput.bamwhen available- reference genome build
- chromosome sizes if bigWig export is needed
Expected Outputs
results/peaks/sample_peaks.narrowPeakor.broadPeakresults/peaks/sample_summits.bedresults/tracks/sample_treat_pileup.bwresults/annotation/peak_annotation.tsvqc/chip_qc_summary.tsv
Starter Pattern
macs3 callpeak \
-t chip.bam \
-c input.bam \
-f BAMPE \
-g hs \
-n sample \
-q 0.01 \
--outdir results/peaks
What ships with it
3 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.
- 12d ago First seen · 171 lines · 32 tokens per session scan A 7de02c2445be
chip-seq is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 32 tokens to every session and 1,281 once invoked, about $0.0002 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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