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 clip-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/clip-peak-calling)<a href="https://agentmods.dev/skills/gptomics/bioskills/clip-peak-calling"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clip-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/clip-peak-calling"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clip-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 | $0.00129 | $0.07450 |
| Opus 5 | $0.00064 | $0.03725 |
| Sonnet 5 | $0.00026 | $0.01490 |
| Haiku 4.5 | $0.00013 | $0.00745 |
Grade A, and why
bio-clip-seq-clip-peak-calling 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 7d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-clip-seq-clip-peak-calling — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 359 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: CLIPper 2.0+, PureCLIP 1.3.1+, Piranha 1.2.1+, omniCLIP 0.2.0+, CTK 1.1.4+, CLAM 1.2+, Paraclu 9+, Skipper (commit 2023.05+), MACS3 3.0+, bedtools 2.31+, samtools 1.19+, idr 2.0.4+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws unexpected errors, introspect the installed binary and adapt the example to match the actual CLI rather than retrying. PureCLIP 2.x changed several flag names; Skipper is distributed as a Snakemake workflow with frequently-evolving paths.
CLIP-seq Peak Calling
"Call protein-RNA binding sites from my deduplicated CLIP BAM" -> Identify regions where read pile-up (and, for iCLIP/eCLIP, single-nucleotide truncations) exceed background from a size-matched input (SMInput) control. The choice of peak caller depends on (a) the CLIP variant (HITS-CLIP, iCLIP, eCLIP, PAR-CLIP), (b) whether SMInput is available, (c) the RBP binding mode (narrow motif vs broad zones vs repeat-binding), and (d) the goal (publication-comparable ENCODE peaks vs single-nucleotide crosslink sites vs high-recall site lists).
- CLI (ENCODE eCLIP canonical):
clipper -b dedup.bam -s hg38 -o peaks.bed --save-pickle --FDR-alpha 0.05 --superlocaltheneclip-norm peaks.bed -i sminput.bamfor log2 fold-change against SMInput (--FDR-alphais the CLIPper flag for the FDR cutoff; older docs sometimes shorten to--FDR) - CLI (single-nucleotide crosslink sites, iCLIP/eCLIP):
pureclip -i dedup.bam -bai dedup.bam.bai -g genome.fa -ibam sminput.bam -ibai sminput.bam.bai -o sites.bed -or regions.bed -nt 8 -dm 8 - CLI (high-recall, beta-binomial windowed; needs SMInput):
SkipperSnakemake workflow with config matching cell type and SMInput BAM - CLI (no SMInput, no truncation):
Piranha -b 50 -p 0.01 -d ZeroTruncatedNegativeBinomial -s -o peaks.bed dedup.bam(Piranha takes the BAM as a positional argument, not via-s) - CLI (CIMS/CITS single-nt from CTK):
tag2cluster.pl dedup.bed cluster.bed --multi-tag-method coverage; thenbedExtractCIMS.pl cluster.bed cims.bed - CLI (multi-mapper rescue for repeat-binding RBPs):
CLAM peakcaller -i unique.bam multimap.bam -o clam_out_dir/ --gtf gencode.gtf(CLAM peakcaller writes peaks into an OUTPUT DIRECTORY, not a single file)
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.
- 7d ago First seen · 359 lines · 129 tokens per session scan A 4c0704d0cfd4
bio-clip-seq-clip-peak-calling is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 129 tokens to every session and 7,450 once invoked, about $0.0006 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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