数据与复现临床医学与医药FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-clinical-databases-somatic-signatures

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.

OpenClawNanoClaw分析处理复现实验bio-clinical-databases-somatic-signatures🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisextract

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-clinical-databases-somatic-signatures

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

Python：SigProfilerExtractor.sigpro() ，用于 de novo signature extraction。
R：MutationalPatterns：：fit_to_signatures() ，用于 fitting to COSMIC signatures。
提取 mutational signatures ，面向 my tumor samples" → Decompose somatic mutation catalogs into mutational signatures (SBS，DBS，ID) to identify DNA damage mechanisms 、 mutagenic processes in cancer genomes. Python：SigProfilerExtractor.sigpro() ，用于 de novo signature extraction R：MutationalPatterns：：fit_to_signatures() ，用于 fitting to COSMIC signatures。
genInstall.install('GRCh38')。

原始文档

SKILL.md 摘录

SigProfiler Workflow

Goal: Extract de novo mutational signatures and decompose to COSMIC reference signatures from somatic VCFs.

Approach: Generate a 96-trinucleotide-context mutation matrix with SigProfilerMatrixGenerator, extract signatures via NMF with SigProfilerExtractor, and fit to COSMIC with SigProfilerAssignment.

Install and Generate Matrix

from SigProfilerMatrixGenerator import install as genInstall
from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen

## Output: SBS96 matrix (96 trinucleotide contexts)

matrices = matGen.SigProfilerMatrixGeneratorFunc(
    project='my_project',
    genome='GRCh38',
    vcfFiles='/path/to/vcf_directory',
    plot=True,
    exome=False  # Set True for WES
)