What is bio-clinical-databases-somatic-signatures?

A bioinformatics workflow for reading somatic VCF files and identifying mutational signatures, which are patterns of DNA changes linked to processes such as faulty DNA repair or UV damage.

Use it to analyse tumour cohorts and assess processes such as BRCA-related homologous-recombination deficiency, mismatch-repair deficiency, APOBEC activity, or tobacco exposure.

It helps connect observed mutations in tumours to the biological or environmental processes that caused them.

bio-clinical-databases-somatic-signatures — Skill for Claude Code and

Install

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.

Any agent

npx skills add GPTomics/bioSkills --skill somatic-signatures

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/somatic-signatures/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/somatic-signatures)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/somatic-signatures"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/somatic-signatures"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/somatic-signatures.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 149 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 7,464 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.07464
Opus 5	$0.00075	$0.03732
Sonnet 5	$0.00030	$0.01493
Haiku 4.5	$0.00015	$0.00746

Measured 7d ago against content hash 0785d4053a8f, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

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 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/sigprofiler_analysis.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-clinical-databases-somatic-signatures — 95% identical, 12 lines differ

clinical-databases/somatic-signatures/SKILL.md · 390 lines

How it starts

The opening of the file, as written. The whole thing — 390 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> then help(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) or extract_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)

Read the full file on GitHub · 390 lines

Files

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.

Changes

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 · 390 lines · 149 tokens per session scan A 0785d4053a8f

Subscribe to this mod's changes

bio-clinical-databases-somatic-signatures is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 149 tokens to every session and 7,464 once invoked, about $0.0007 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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