copy-number-variation
There are 67 repositories under copy-number-variation topic.
sigven/pcgr
Personal Cancer Genome Reporter (PCGR)
gavinha/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
AntonioDeFalco/SCEVAN
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.
imgag/ClinCNV
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
Genotek/ClassifyCNV
ClassifyCNV: a tool for clinical annotation of copy-number variants
flowhub-team/CNV
Copy Number Variation
ShixiangWang/DoAbsolute
:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
DKFZ-ODCF/ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
pughlab/VisCap
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.
cbg-ethz/SCICoNE
Single-cell copy number calling and event history reconstruction.
vicsanga/Postre
POSTRE: Prediction Of STRuctural variant Effects
rezacsedu/Neural-Ensemble-Method-for-Cancer-Prediction
A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations
OpenOmics/genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
caravagnalab/CNAqc
CNAqc - Copy Number Alteration (CNA) Quality Check package
bio-ontology-research-group/DeepSVP
Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
oicr-gsi/sequenza
Workflow for Sequenza, cellularity and ploidy
TimD1/nPoRe
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
cbg-ethz/SCATrEx
Map single-cell transcriptomes to copy number evolutionary trees.
nriddiford/cnvPlotteR
Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec
mskcc/facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
dpastling/plethora
Copy number estimation of highly duplicated sequences
ohdongha/OrthNet
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
bihealth/cnvetti
:tada: CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data
samabs/conliga
Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)
bernatgel/CopyNumberPlots
R package to create plots representing copy number data using karyoploteR
jakob-he/TADA
TAD-aware annotation of CNVs
rptashkin/facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
VCCRI/ConanVarvar
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole genome sequencing data
piyalkarum/rCNV
An R package for detecting copy number variants from SNPs data
RRafiee/XHMM
eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data
skoc/bcpm-pfda-challenge
My Solution for PrecisionFDA Brain Cancer Predictive Modeling and Biomarker Discovery Challenge
akiomiyao/ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
KrasnitzLab/CNVMetrics
R Package to compare copy number variant (CNV) results from multiple samples/methods
XUKEREN/phd-pipeline
Some workflows I wrote for my phd projects