SCoNEs is an R package designed to estimate Copy Number Variations (CNVs) in whole genome sequencing (WGS) data from tumor-normal paired samples. Utilizing a read depth approach, SCoNEs accurately identifies regions of genomic amplification or deletion, aiding in the comprehensive analysis of cancer genomes.

Key Features:

• Read Depth Analysis: Employs read depth information from WGS data to detect CNVs, providing a reliable method for identifying copy number changes.
• Tumor-Normal Pairing: Analyzes paired tumor and normal samples to distinguish somatic CNVs from germline variations, enhancing the specificity of CNV detection.
• User-Friendly Interface: Offers an accessible platform for researchers to perform CNV analysis without extensive computational expertise.

Availability: SCoNEs is free and open-source, released under the MIT License. Researchers can access and contribute to its development through the GitHub repository.

Note: All resources and documentation are provided in English.

By leveraging read depth information in tumor-normal paired WGS data, SCoNEs offers a robust tool for accurate CNV detection, facilitating advancements in cancer genomics research.