Personal Cancer Genome Reporter (PCGR)

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.

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

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

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

Copy Number Variation

📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Allele-specific copy number estimation with whole genome sequencing

Single-cell copy number calling and event history reconstruction.

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.

POSTRE: Prediction Of STRuctural variant Effects

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

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Workflow for Sequenza, cellularity and ploidy

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

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Map single-cell transcriptomes to copy number evolutionary trees.