Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

Pipeline for running the FACETS copy number caller using Snakemake

Genome Alteration Print (GAP)

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data

Easy Copy Number !

Processing DNA Copy Number (CN) Data for Detection of CN Events

CNprep Package - Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Copy Number tree utilities (CNtu)

Lifterover copy number segments in whole

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Copy number calling and variant classification using targeted short read sequencing