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 PKU-YuanGroup/OpenAI4S --skill bio-clip-seq-crosslink-site-detectiongit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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-crosslink-site-detection)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clip-seq-crosslink-site-detection"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clip-seq-crosslink-site-detection/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-crosslink-site-detection"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clip-seq-crosslink-site-detection.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 | $0.00117 | $0.05616 |
| Opus 5 | $0.00059 | $0.02808 |
| Sonnet 5 | $0.00023 | $0.01123 |
| Haiku 4.5 | $0.00012 | $0.00562 |
Grade A, and why
bio-clip-seq-crosslink-site-detection 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 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.
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
100% identical to bio-clip-seq-crosslink-site-detection — 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 — 268 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: PureCLIP 1.3.1+, CTK 1.1.4+, PARalyzer 1.5+, wavClusteR 2.34+, pyCRAC 1.5+, samtools 1.19+, bedtools 2.31+, pysam 0.22+, R 4.3+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags - Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_nameto verify parameters
If code throws unexpected errors, introspect the installed tool and adapt the example to match the actual CLI rather than retrying.
CLIP-seq Crosslink-Site Detection
"Detect single-nucleotide crosslink sites in my CLIP data" -> Identify the exact base where the protein-RNA UV adduct caused the reverse transcriptase to stop (truncation, in iCLIP/eCLIP), to read through with a mutation (deletion in HITS-CLIP, T->C in PAR-CLIP), or to leave a multi-base signature (PARalyzer kernel density for PAR-CLIP). Single-nucleotide resolution is the foundation of motif registration (mCross), allele-specific binding (BEAPR/ASPRIN), variant-effect prediction, and the most rigorous comparisons across CLIP variants. The detection chemistry differs by CLIP type: iCLIP/eCLIP read 5' end is one nucleotide downstream of the crosslink (CITS); PAR-CLIP reads contain T->C transitions at the crosslink (CIMS substitution); HITS-CLIP reads contain deletions at the crosslink (CIMS deletion).
- CLI (HMM, all CLIP variants):
pureclip -i dedup.bam -bai dedup.bam.bai -g genome.fa -ibam sminput.bam -ibai sminput.bam.bai -o crosslinks.bed -or regions.bed -nt 8 -dm 8 - CLI (CTK CITS truncations, iCLIP/eCLIP):
parseAlignment.pl --map-qual 1 --min-len 18 --mutation-file mut.txt dedup.bam dedup.bedthentag2cluster.pl ... -cs5 5 -m 1for truncation-cluster - CLI (CTK CIMS deletions, HITS-CLIP):
getMutationType.pl dedup.bed mut.txt -type delthenCIMS.pl dedup.bed mut.txt -big -c -p 0.01 cims.bed - CLI (CTK CIMS T->C, PAR-CLIP):
getMutationType.pl dedup.bed mut.txt -type sub -nuc t -mut cthenCIMS.pl dedup.bed t2c.mut -p 0.001 t2c_cims.bed - CLI (PAR-CLIP kernel density):
PARalyzer params.ini(parameters file defines read length, min reads per cluster, mutation rate threshold) - CLI (PAR-CLIP wavClusteR R):
wavClusteR::filterClusters(cl, snps=NULL, filterFC=FALSE)after wavelet clustering
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 · 268 lines · 117 tokens per session scan A 8f10ef702d68
bio-clip-seq-crosslink-site-detection is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 117 tokens to every session and 5,616 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. It is 100% identical to bio-clip-seq-crosslink-site-detection, differing in 12 lines, and is treated as a copy.
Other skills, from other repositories
boltz-structure-prediction
Boltz-1 / Boltz-2 structure prediction for proteins, complexes, and ligand-aware validation. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC…
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
flow-cytometry-analysis
Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw FCS parsing only use flowio.
scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review…
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
glycobiology
Glycosylation site prediction and glycobiology analysis. N-glycosylation motif finding, O-glycosylation hotspot prediction, glycan structure resources. Lightweight, pure Python. For protein function queries use uniprot-database; for structure analysis use alphafold-database.