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lgmgeo /AnnotSV

Star246

Annotation and Ranking of Structural Variation

annotation genetics ngs ranking cnv sv priorization

UpdatedMar 6, 2025
Tcl

ShixiangWang /sigminer

Star150

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

visualization bioinformatics r somatic-variants easy-to-use sbs somatic-mutations cnv nmf cancer-research dbs mutational-signatures copynumber-signatures indel signature-extraction nmf-extraction cosmic-signatures bayesian-nmf

UpdatedOct 12, 2024
R

icbi-lab /infercnvpy

Star148

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

single-cell cnv scverse

UpdatedMar 10, 2025
Python

XWangLabTHU /cfDNApipe

Star63

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

snv cnv cfdna wgs-data cell-free-dna virus-detection wgbs-data

UpdatedAug 18, 2022
Python

Genotek /ClassifyCNV

Star61

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

bioinformatics annotations duplication pathogenicity cnv copy-number-variation deletion clinical-genomics

UpdatedJun 26, 2023
Python

flowhub-team /CNV

Star58

Copy Number Variation

genomics genome cnv copy-number-variation copynumbervariation

UpdatedJun 28, 2023

PacificBiosciences /HiFiCNV

Star40

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

cnv hifi pacbio-ccs

UpdatedOct 22, 2024
Shell

single-cell-genetics /XClone

Star36

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

cancer-genomics cnv single-cell-rna-seq single-cell-analysis cnv-detection spatial-transcriptomics cna-detection

UpdatedMar 13, 2025
Python

Illumina /witty.er

Star32

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

benchmarking variants cnv copy-number-variation variant-analysis structural-variation

UpdatedSep 13, 2023
C#

zhouzilu /iCNV

Star26

Integrated copy number variation detection toolset

r-package wgs cnv wes muti-platform snp-array

UpdatedFeb 12, 2020
R

oicr-gsi /sequenza

Star19

Workflow for Sequenza, cellularity and ploidy

workflow rnaseq cnv copy-number-variation cnv-detection cnv-analysis

UpdatedMar 14, 2025
R

nf-cmgg /structural

Star19

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

annotation repeats ngs cnv cram structural-variation ngs-pipeline nextflow-pipeline short-reads

UpdatedFeb 21, 2025
Nextflow

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.

cnv targeted-sequencing