lima1/PureCN

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

Analysis pipeline for cancer sequencing data

Copy number variant detection from targeted DNA sequencing

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Personal Cancer Genome Reporter (PCGR)

Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

dN/dS methods to quantify selection in cancer and somatic evolution