cnv
There are 2 repositories under cnv topic.
- Language:Tcl 193
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
Language:R 137icbi-lab / infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
Language:Python 118Genotek / ClassifyCNV
ClassifyCNV: a tool for clinical annotation of copy-number variants
Language:Python 57XWangLabTHU / cfDNApipe
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
Language:Python 55- HiFiCNV
PacificBiosciences / HiFiCNV
Copy number variant caller and depth visualization utility for PacBio HiFi reads
Language:Shell 32 Illumina / witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
Language:C# 26- Language:R 25
single-cell-genetics / XClone
Detection of allele-specific subclonal copy number variations from single-cell transcriptomic data.
Language:Python 18- Language:R 15
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.
Language:R 14- Language:C 12
TheJacksonLaboratory / JAX-CNV
Official code repository for JAX-CNV
Language:C++ 12- Language:Perl 10
matheuscburger / Excavator2
A fork of the project Excavator2 from sourceforge.
Language:R 9galantelab / sideRETRO
A pipeline for detecting Somatic Insertion of DE novo RETROcopies
Language:C 7joommf / oommf-extension-dmi-cnv
Dzyaloshinskii-Moriya interaction for crystallographic class Cnv
Language:C++ 6RRafiee / XHMM
eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data
Language:Shell 6KrasnitzLab / CNVMetrics
R Package to compare copy number variant (CNV) results from multiple samples/methods
Language:R 5nf-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
Language:Nextflow 5redndgreen8 / hmcnc
Hidden Markov Model based Copy number caller
Language:Python 5vidhurva / Random-Forest-Copy-Number-Variation
Bioinformatics CNV Detection with Random Forest Model
Language:Python 5- Language:Perl 4
assane-mbodj / dupfinder
DupFinder: A tools to detect the duplicated genes using Illumina and Nanopore sequencing data
Language:Nextflow 4Genalice / genalice-icr96
Materials & Methods for CNV calling with Genalice software against a benchmark dataset
Language:Shell 4- Language:Python 4
- Language:Perl 4
- Language:Python 4
- Language:C++ 4
biomystery / atacCNV
A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data
Language:R 3hernanmd / PennCNV.Illumina
Workflow for running PennCNV with Illumina platform final report
Language:Shell 3latouchek / mtv-vsphere
Walk through Red Hat MTV
Language:Shell 3msls-bioinfo / CmiRClustFinder_v1.0
CmiRClustFinder v1.0: a tool for identification of CNV co-locolized miRNA, miRNA clusers and genes in TCGA cancer cohorts.
Language:R 3- OCT-Scans-Classification
SaeedShurrab / OCT-Scans-Classification
This project compares two learning paradigm, namely transfer-learning and self-supervised learning in a classification task of three retina disorders CNV, DME and DUSEN in addition to the normal condition using an OCT B-scans
Language:Jupyter Notebook 3 - PYRUS
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.
Language:R 3
