cnv
There are 91 repositories under cnv topic.
lgmgeo/AnnotSV
Annotation and Ranking of Structural Variation
ShixiangWang/sigminer
🌲 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
icbi-lab/infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
XWangLabTHU/cfDNApipe
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
Genotek/ClassifyCNV
ClassifyCNV: a tool for clinical annotation of copy-number variants
flowhub-team/CNV
Copy Number Variation
PacificBiosciences/HiFiCNV
Copy number variant caller and depth visualization utility for PacBio HiFi reads
single-cell-genetics/XClone
Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
zhouzilu/iCNV
Integrated copy number variation detection toolset
nf-cmgg/structural
A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
oicr-gsi/sequenza
Workflow for Sequenza, cellularity and ploidy
beroukhim-lab/ascets
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.
jia-zhuang/mapper
Short reads aligner for NIPT/CNV
TheJacksonLaboratory/JAX-CNV
Official code repository for JAX-CNV
dpastling/plethora
Copy number estimation of highly duplicated sequences
galantelab/sideRETRO
A pipeline for detecting Somatic Insertion of DE novo RETROcopies
joommf/oommf-extension-dmi-cnv
Dzyaloshinskii-Moriya interaction for crystallographic class Cnv
matheuscburger/Excavator2
A fork of the project Excavator2 from sourceforge.
vidhurva/Random-Forest-Copy-Number-Variation
Bioinformatics CNV Detection with Random Forest Model
latouchek/mtv-vsphere
Walk through Red Hat MTV
lindenb/x11hts
X11 related utilities for hts
redndgreen8/hmcnc
Hidden Markov Model based Copy number caller
RRafiee/XHMM
eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data
akiomiyao/ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
assane-mbodj/dupfinder
DupFinder: A tools to detect the duplicated genes using Illumina and Nanopore sequencing data
Genalice/genalice-icr96
Materials & Methods for CNV calling with Genalice software against a benchmark dataset
HaoKuo/ctCNV
A new CNV calling method for DNA-seq data
haoziyeung/somatic_pipeline
肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）
jingxinfu/TCGAdnloader
TCGA hg19 and hg38 data downloader.
KrasnitzLab/CNVMetrics
R Package to compare copy number variant (CNV) results from multiple samples/methods
robinjugas/CNproScan
CNV detection for prokaryote genomes using NGS sequencing data
TNTurnerLab/PYRUS
PYRUS is a plotting tool that uses tabix files to create line graphs from bed file data. Utilization of PYRUS includes having a quick plotter for copy number variation within a given chromosomal range of a referenced bed file.
brj0/mepylome
Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files
msls-bioinfo/CmiRClustFinder_v1.0
CmiRClustFinder v1.0: a tool for identification of CNV co-locolized miRNA, miRNA clusers and genes in TCGA cancer cohorts.
oicr-gsi/hmmcopy
Calls Copy Number Variants on sequencing data from cancer patients