CopyNumberEngine

Somatic Copy Number Alteration Analysis Pipeline

A pure-Python pipeline for somatic CNA analysis including CBS segmentation, ploidy/purity estimation, and NMF signature extraction.

Features

• Segmentation (Circular Binary Segmentation, CBS-style)
• Ploidy and purity estimation (grid search optimization)
• Focal vs arm-level CNA classification
• Aneuploidy score computation
• CNA signature extraction (NMF, 3 signatures)

Results

• 100 tumors × 2000 genomic bins (500kb resolution)
• Mean estimated ploidy: 3.32 ± 1.15
• Mean aneuploidy score: 0.508 ± 0.152
• Total segments detected: 2155
• Median segment size: 10.0 Mb

Usage

pip install numpy scipy matplotlib
python copy_number_engine.py

Tags

copy-number aneuploidy chromosomal-instability cna-calling allele-specific cbs-segmentation