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-clinical-databases-somatic-signaturesgit 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-clinical-databases-somatic-signatures)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clinical-databases-somatic-signatures"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-somatic-signatures/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-clinical-databases-somatic-signatures"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-somatic-signatures.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 | $0.00149 | $0.07540 |
| Opus 5 | $0.00075 | $0.03770 |
| Sonnet 5 | $0.00030 | $0.01508 |
| Haiku 4.5 | $0.00015 | $0.00754 |
Grade A, and why
bio-clinical-databases-somatic-signatures 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
95% identical to bio-clinical-databases-somatic-signatures — 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 — 398 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: SigProfilerMatrixGenerator 1.2+ (Bergstrom 2019), SigProfilerExtractor 1.1.24+ (Islam 2022), SigProfilerAssignment 0.1+ (Diaz-Gay 2023), MutationalPatterns 3.12+ (Manders 2022), MuSiCal 0.7+ (Jin 2024), SigNet (Serrano 2023, bioRxiv), HRDetect (Davies 2017 / Degasperi 2022 implementations), pandas 2.2+, R 4.3+. COSMIC v3.4 (2023, COSMIC v98): 86 SBS, 11 DBS, 18 ID, 21 CN, 16 SV signatures (v3.6 is the current catalog as of 2026).
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_name
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. COSMIC signature naming evolves: SBS40 was split to SBS40a/b/c in v3.4 (Senkin 2024); SBS17 split to SBS17a/b (5-FU); SBS10 split to SBS10a-d (POLE/POLD1).
Somatic Mutational Signatures; Etiology, Extraction, Clinical Use
'Extract mutational signatures from this tumor cohort and identify HRD/MMR/APOBEC processes' -> Generate 96-context (or DBS/ID/CN/SV) matrix from VCF; choose de novo extraction (NMF) vs refit-to-COSMIC by cohort size; map dominant signatures to etiology; flag clinical actionability.
- Python (recommended): SigProfilerMatrixGenerator -> SigProfilerExtractor (de novo) or SigProfilerAssignment (refit)
- R alternative:
MutationalPatterns::fit_to_signatures()(strict refit) orextract_signatures()(NMF de novo) - Python (mvNMF for non-uniqueness): MuSiCal (Jin 2024 Nat Genet)
- Python (deep learning low-mutation count): SigNet (Serrano 2023)
- R (HRD-specific): HRDetect (Davies 2017 Nat Med); the 6-feature BRCA-deficiency classifier
COSMIC v3.4 Catalog: Evolution and Composition
| Class | Count | Encoding |
|---|---|---|
| SBS (Single Base Substitutions) | 86 | 96 trinucleotide contexts (6 substitution types x 16 trinucleotides) |
| DBS (Doublet Base Substitutions) | 11 | 78 strand-agnostic doublet classes (Bergstrom 2019) |
| ID (Insertion/Deletion) | 18 | 83 categories (indel length x repeat context x microhomology) |
| CN (Copy Number) | 21 | 48 channels (total CN x heterozygosity x segment length; Steele 2022 Nature) |
| SV (Structural Variants) | 16 | 32 channels (cluster x length x type) |
What ships with it
3 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 · 398 lines · 149 tokens per session scan A 70fec447696e
bio-clinical-databases-somatic-signatures is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 149 tokens to every session and 7,540 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-clinical-databases-somatic-signatures, differing in 12 lines, and is treated as a copy.
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