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 GPTomics/bioSkills --skill atac-peak-callinggit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/atac-peak-calling)<a href="https://agentmods.dev/skills/gptomics/bioskills/atac-peak-calling"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/atac-peak-calling/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/gptomics/bioskills/atac-peak-calling"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/atac-peak-calling.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 | $0.00093 | $0.05949 |
| Opus 5 | $0.00046 | $0.02975 |
| Sonnet 5 | $0.00019 | $0.01190 |
| Haiku 4.5 | $0.00009 | $0.00595 |
Grade A, and why
bio-atac-seq-atac-peak-calling scanned grade A with 1 finding 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 9d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget https://github.com/Boyle-Lab/Blacklist/raw/master/lists/hg38-blacklist.v2.bed.gz Copies of this mod
1 near-identical copy found in the catalogue:
- bio-atac-seq-atac-peak-calling — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 321 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: MACS3 3.0.2+, MACS2 2.2.9+, Genrich 0.6.1+, HMMRATAC 1.2+ (now bundled in MACS3 as macs3 hmmratac), samtools 1.19+, bedtools 2.31+, IDR 2.0.4+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws unexpected errors, introspect the installed binary (<tool> -h) and adapt the example to match the actual CLI rather than retrying.
ATAC-seq Peak Calling
"Call accessible regions from my ATAC-seq BAM" -> Identify Tn5-hypersensitive open chromatin, treating fragments as point insertion events (not protein-bound regions as in ChIP-seq) and accounting for the lack of input control.
- CLI (canonical, ENCODE 4):
macs2 callpeak -t atac.bam -f BAM -g hs -n sample --nomodel --shift -75 --extsize 150 --keep-dup all -B --SPMR -p 0.01(use-f BAM, not-f BAMPE-- BAMPE reads true fragment ends and ignores--shift/--extsize) - CLI (HMM-based, single sample):
macs3 hmmratac -i atac.bam -n sample --outdir hmm_out - CLI (joint replicates):
Genrich -j -t rep1.bam,rep2.bam -o peaks.narrowPeak -e chrM -E blacklist.bed
The -p 0.01 (loose) plus IDR is the ENCODE pattern: low stringency increases peak overlap between replicates, and IDR rescues the reproducible set. Single-sample workflows usually swap to -q 0.05 instead.
Algorithmic Taxonomy
| Tool | Model | Treats fragments as | Min reps | Strength | Fails when |
|---|---|---|---|---|---|
| MACS3/MACS2 | Local Poisson lambda + FDR | Point-source insertions (+/- shift) | 1 | Mature, ENCODE-default, fast, narrow + broad modes | Confounds NFR with broad accessible domains; no input means lambda from local genome only |
| Genrich (ATAC mode -j) | q-value on log-transformed p-value, joint replicate model | Whole fragments (paired-end intervals) | 1 (multi-rep optional) | Treats reps jointly; can exclude chrM via -e chrM; auto blacklist via -E; PCR-dup removal via -r |
Less peer-reviewed than MACS; thin literature; slow on deep libraries |
| MACS3 hmmratac (was HMMRATAC) | 3-state HMM (open / nucleosomal / background) on fragment-size signal | Fragment-size classes | 1 | Models nucleosome periodicity directly; differentiates NFR and flanking nucleosomes | Needs >= 30M de-duplicated nuclear reads; memory-hungry; slow; flat fragment distribution -> garbage HMM |
HOMER findPeaks -style dnase |
Fixed window + fold-change cutoff | Tag positions | 1 | Convenient for downstream HOMER motif analysis | Less calibrated p-values than MACS; window-size sensitive |
| nf-core/atacseq | Wrapper (MACS2 by default) | Same as MACS2 | 1 | Reproducible Nextflow pipeline with QC built in | Only as good as the underlying caller |
What ships with it
2 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.
- 9d ago First seen · 321 lines · 93 tokens per session scan A aaf79f23f81d
bio-atac-seq-atac-peak-calling is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 93 tokens to every session and 5,949 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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