Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.
Ahmed Ibrahim Samir KhalilCosterwell KhyriemAnupam ChattopadhyayAmartya SanyalPublished in: BMC bioinformatics (2020)
CNAtra is a single-sample CNA detection tool that provides an analytical and visualization framework for CNA profiling without relying on any reference control. It can detect chromosome-level segmental aneuploidies and high-confidence focal alterations, even from low-coverage data. CNAtra is an open-source software implemented in MATLAB®. It is freely available at https://github.com/AISKhalil/CNAtra.
Keyphrases
- copy number
- mitochondrial dna
- genome wide
- dna methylation
- affordable care act
- papillary thyroid
- small molecule
- electronic health record
- squamous cell
- data analysis
- big data
- high throughput
- loop mediated isothermal amplification
- liquid chromatography
- gene expression
- machine learning
- squamous cell carcinoma
- health insurance
- label free
- mass spectrometry
- deep learning