Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4Snpx agentmods add skills/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotationWrote 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/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotation)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotation"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotation/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/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotation"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clip-seq-binding-site-annotation.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 | $0.00142 | $0.06007 |
| Opus 5 | $0.00071 | $0.03003 |
| Sonnet 5 | $0.00028 | $0.01201 |
| Haiku 4.5 | $0.00014 | $0.00601 |
Grade A, and why
bio-clip-seq-binding-site-annotation 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.
This is a copy
95% identical to bio-clip-seq-binding-site-annotation — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 337 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: ChIPseeker 1.40+, RCAS 1.30+, GenomicFeatures 1.56+, GenomicRanges 1.56+, rbp-maps (Yeo github), bedtools 2.31+, pybedtools 0.10+, pyranges 0.0.129+.
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('<pkg>')then?function_nameto verify parameters - 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 package and adapt the example to match the actual API rather than retrying. ChIPseeker 1.40+ changed the priority defaults; verify the priority vector before pipelining.
Binding Site Annotation
"Annotate where in transcripts my RBP binds" -> Map CLIP peaks or single-nucleotide crosslink sites to RNA features and report the per-feature distribution. The interpretation is RBP-class-specific: splicing factors (PTBP1, U2AF2, RBFOX) bind intron-exon junctions; mRNA-stability regulators (HuR, PUM2) bind 3' UTRs; translation factors (EIF3J, RPS19) bind 5' UTRs and CDS; and small-ncRNA-binding RBPs (NSUN2 tRNAs, LARP7 7SK, TROVE2 Y-RNAs) bind specific non-coding transcripts. A correct annotation pipeline (a) resolves overlapping features by priority, (b) preserves transcript-isoform context, (c) generates metagene distributions, and (d) flags repeat-element overlap separately.
- R (peak-level, fast):
ChIPseeker::annotatePeak(peaks, TxDb=txdb, level='gene', tssRegion=c(-100,100))thenplotAnnoPie(anno) - R (transcript-level with RNA-specific regions): RCAS
runReport(queryRegions=peaks, gffData=gencode_gtf, genomeVersion='hg38') - CLI (regions only):
bedtools intersect -s -wa -wb -a peaks.bed -b features.bed(manual hierarchy) - R (splicing-regulatory map for splice factors): RBP-Maps (
yeolab/rbp-maps) generates the 1400 nt vectorized cassette-exon map used in Yeo lab ENCODE papers - CLI (metagene aggregation):
deepTools computeMatrixor RSeQCgeneBody_coverage.pyfor read profiles
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.
- 8d ago First seen · 337 lines · 142 tokens per session scan A 1efe5031c69b
bio-clip-seq-binding-site-annotation is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed today), licensed MIT. It adds 142 tokens to every session and 6,007 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-clip-seq-binding-site-annotation, differing in 12 lines, and is treated as a copy.
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