Annotation and Ranking of Structural Variation

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

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

Joint structural variant and copy number variant caller for HiFi sequencing data

Copy Number Variation

Copy number variant caller and depth visualization utility for PacBio HiFi reads

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

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

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Integrated copy number variation detection toolset

Workflow for Sequenza, cellularity and ploidy

This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data.

Short reads aligner for NIPT/CNV

Official code repository for JAX-CNV

A fork of the project Excavator2 from sourceforge.

Copy number estimation of highly duplicated sequences

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

Dzyaloshinskii-Moriya interaction for crystallographic class Cnv