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-alternative-splicing-splicing-quantificationgit 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-alternative-splicing-splicing-quantification)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alternative-splicing-splicing-quantification"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alternative-splicing-splicing-quantification/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-alternative-splicing-splicing-quantification"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alternative-splicing-splicing-quantification.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 | $0.00187 | $0.07243 |
| Opus 5 | $0.00093 | $0.03622 |
| Sonnet 5 | $0.00037 | $0.01449 |
| Haiku 4.5 | $0.00019 | $0.00724 |
Grade A, and why
bio-splicing-quantification 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.
This is a copy
97% identical to bio-splicing-quantification — 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 — 385 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: rMATS-turbo 4.3+, SUPPA2 2.4+, leafcutter 0.2.9+, MAJIQ 3.0+, IRFinder-S 2.0+, kallisto 0.50+, Salmon 1.10+, pandas 2.2+, STAR 2.7.11+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_nameto verify parameters - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Splicing Quantification
Quantify alternative splicing events as PSI (percent spliced in) from RNA-seq. PSI = inclusion read evidence / (inclusion + skipping read evidence), normalized for differential mapping opportunity between isoforms. The choice of quantification unit (event, intron cluster, LSV, transcript) determines which biological questions can be answered and which failure modes apply.
Algorithmic Taxonomy
| Family | Unit | Reference tools | Fails when |
|---|---|---|---|
| Event-based | Pre-defined SE/A5SS/A3SS/MXE/RI events from annotation | rMATS-turbo, SUPPA2, VAST-TOOLS | Event isn't in annotation; complex multi-junction events split arbitrarily; AFE/ALE confounded with splicing |
| LSV-based | Local Splice Variations at single source/target nodes | MAJIQ V3 | Memory-constrained environments; cohorts smaller than ~3 reps; non-academic users (license) |
| Junction-cluster | Annotation-free intron clusters by shared splice sites | leafcutter, leafcutter2 | Undersampled clusters lose power; topology biologically uninterpretable for novel events |
| Splice-graph | Graph nodes (non-overlapping exonic regions) | Whippet, Shiba | Whippet maintenance status uncertain since ~2022; complex multi-exon graphs |
| Coverage-aware (IR) | Intron body coverage + flanking junctions | IRFinder-S, S-IRFindeR, iREAD | Confounded by overlapping exons, repeats, low mappability regions |
| Isoform-based | Transcript abundance via EM | Salmon/kallisto + tximport | Salmon EM uncertainty propagates; many similar isoforms (TTN, MAPT) become indistinguishable |
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.
- 12d ago First seen · 385 lines · 187 tokens per session scan A a72e3ca29697
bio-splicing-quantification is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (403 stars, last pushed today), licensed MIT. It adds 187 tokens to every session and 7,243 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-splicing-quantification, differing in 12 lines, and is treated as a copy.
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