Personal Cancer Genome Reporter (PCGR)

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

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

ClassifyCNV: a tool for clinical annotation of copy-number variants

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package

Allele-specific copy number estimation with whole genome sequencing

A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations

CNAqc - Copy Number Alteration (CNA) Quality Check package

Clinical Whole Genome and Exome Sequencing Pipeline

Single-cell copy number calling and event history reconstruction.

Galaxy Tool Shed repositories maintained and developed by the Morin Lab.

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity

eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data

Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

Tool for calling tumour-specific somatic copy number alterations from targeted sequencing data. This tool is based on the germline copy number variant caller published by Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

IhybCNV: An intra-hybrid approach for CNV detection from next-generation sequencing data