copy-number-variation

There are 2 repositories under copy-number-variation topic.

sigven / pcgr
Personal Cancer Genome Reporter (PCGR)
cancer-genomics cancer-variants somatic interpreter reporting-engine clinical oncology-data precision-oncology vcf tumor annotation-framework annotation-tool cancer copy-number-variation snvs therapeutic-targets precision-cancer-medicine variant-interpretation
Language:R 244
gavinha / TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity
Language:R 89
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.
single-cell copy-number-variation copynumber subclonal-deconvolution subclone-identification clonal-evolution clonal-analysis microenvironment tumor-heterogeneity tumor-classification tumor-evolution scrna-seq-analysis scrna-pipeline scrna-seq aneuploidy
Language:HTML 78
imgag / ClinCNV
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
bioinformatics-tool bioinformatics-algorithms copy-number-variation
Language:R 68
flowhub-team / CNV
Copy Number Variation
cnv copy-number-variation copynumbervariation genome genomics
59
Genotek / ClassifyCNV
ClassifyCNV: a tool for clinical annotation of copy-number variants
bioinformatics cnv copy-number-variation annotations duplication deletion clinical-genomics pathogenicity
Language:Python 58
ShixiangWang / DoAbsolute
:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
absolute copy-number-variation firehose
Language:R 34
Illumina / witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
benchmarking variant-analysis variants structural-variation copy-number-variation cnv
Language:C# 26
DKFZ-ODCF / ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
copy-number-variation gc-correction genome-sequencing roddy structural-variation workflow
Language:R 24
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.
copy-number-variation germline
Language:R 22
cbg-ethz / SCICoNE
Single-cell copy number calling and event history reconstruction.
bayesian-inference single-cell copy-number-variation cancer-genomics mcmc
Language:C++ 20
rezacsedu / Neural-Ensemble-Method-for-Cancer-Prediction
A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations
cancer-genomics deeplearning neural-networks copy-number-variation classification tcga cnv-data conv-lstm cae
Language:Jupyter Notebook 19
vicsanga / Postre
POSTRE: Prediction Of STRuctural variant Effects
copy-number-variation medical-genetics non-coding-variants structural-variants cnvs pathogenic-variants pathogenicity
Language:R 17
bio-ontology-research-group / DeepSVP
Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
copy-number-variation ontology structural-variation
Language:Python 16
TimD1 / nPoRe
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
nanopore variant-calling long-reads ont-data genomics alignment tandem-repeats copy-number-variation
Language:Python 16
oicr-gsi / sequenza
Workflow for Sequenza, cellularity and ploidy
rnaseq copy-number-variation cnv cnv-detection cnv-analysis
Language:R 15
caravagnalab / CNAqc
CNAqc - Copy Number Alteration (CNA) Quality Check package
copy-number-variation quality-check genomics karyotype peak-detection
Language:R 14
OpenOmics / genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
copy-number-variation germline-variants quality-control structural-variants singularity snakemake whole-genome-sequencing somatic-variants pipeline hla-typing variant-annotation variant-effect-prediction whole-exome-sequencing
Language:Python 14
cbg-ethz / SCATrEx
Map single-cell transcriptomes to copy number evolutionary trees.
cancer-genomics scrna-seq copy-number-variation jax
Language:Python 13
nriddiford / cnvPlotteR
Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec
cancer-genomics cnv-data cnv-seq control-freec copy-number-variation genome
Language:R 12
dpastling / plethora
Copy number estimation of highly duplicated sequences
plethora genome genomics cnv next-generation-sequencing copy-number-variation duf1220
Language:Perl 10
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
co-linearity comparative-genomics convergent-evolution copy-number-variation duplication evolution orthologs structural-variation synteny transposition
Language:Python 9
bihealth / cnvetti
:tada: CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data
bioinformatics copy-number-variation next-generation-sequencing
Language:Rust 8
samabs / conliga
Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)
bayesian-methods bayesian-inference copy-number copy-number-variation probabilistic-models probabilistic-graphical-models mcmc r rcpparmadillo bayesian-nonparametric-models genomics
Language:C++ 8
bernatgel / CopyNumberPlots
R package to create plots representing copy number data using karyoploteR
bioconductor bioconductor-package bioinformatics copy-number-variation genomics genomics-visualization r r-package rstats
Language:R 6
jakob-he / TADA
TAD-aware annotation of CNVs
copy-number-variation cnvs machine-learning pathogenicity annotation
Language:Python 6
rptashkin / facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
copy-number-variation somatic-variants ngs ngstools ngs-analysis
Language:R 6
RRafiee / XHMM
eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data
copy-number-variation cnv pca pca-analysis hidden-markov-model xhmm deletion duplication exome exomes pipeline next-generation-sequencing ngs
Language:Shell 6
VCCRI / ConanVarvar
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole genome sequencing data
bioinformatics genomics copy-number-variation
Language:R 6
broadinstitute / tangent
copy-number-variation cancer-genomes sequencing-coverage analysis-algorithms
Language:Shell 5
KrasnitzLab / CNVMetrics
R Package to compare copy number variant (CNV) results from multiple samples/methods
r metrics cnv copy-number-variation package r-language r-package
Language:R 5
piyalkarum / rCNV
An R package for detecting copy number variants from SNPs data
cnv-analysis genetics genomics landscape-genetics snps copy-number-variation cran gene-duplication r
Language:R 5
akiomiyao / ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
polymorphism inversion insertion ngs deletion snp k-mer ngstools alignment-free-algorithm somatic-mutations genotype sequence-alignments variant cnv copy-number-variation crispr-cas9
Language:Perl 4
mskcc / facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
copy-number-variation ngs ngs-analysis allele-specific
Language:R 4
Seborinos / NCutYX
NCutYX is an R package for clustering different types of genomic data.
clustering cancer-genomics graph-cut graphs graph-algorithms gene-expression copy-number-variation r rcpp devtools c-plus-plus proteins
Language:R 4
skoc / bcpm-pfda-challenge
My Solution for PrecisionFDA Brain Cancer Predictive Modeling and Biomarker Discovery Challenge
biomarker boosting-algorithms brain-cancer copy-number-variation feature-selection gene-expression machine-learning
Language:R 4

copy-number-variation

sigven / pcgr

gavinha / TitanCNA

AntonioDeFalco / SCEVAN

imgag / ClinCNV

flowhub-team / CNV

Genotek / ClassifyCNV

ShixiangWang / DoAbsolute

Illumina / witty.er

DKFZ-ODCF / ACEseqWorkflow

pughlab / VisCap

cbg-ethz / SCICoNE

rezacsedu / Neural-Ensemble-Method-for-Cancer-Prediction

vicsanga / Postre

bio-ontology-research-group / DeepSVP

TimD1 / nPoRe

oicr-gsi / sequenza

caravagnalab / CNAqc

OpenOmics / genome-seek

cbg-ethz / SCATrEx

nriddiford / cnvPlotteR

dpastling / plethora

ohdongha / OrthNet

bihealth / cnvetti

samabs / conliga

bernatgel / CopyNumberPlots

jakob-he / TADA

rptashkin / facets2n

RRafiee / XHMM

VCCRI / ConanVarvar

broadinstitute / tangent

KrasnitzLab / CNVMetrics

piyalkarum / rCNV

akiomiyao / ped

mskcc / facets2n

Seborinos / NCutYX

skoc / bcpm-pfda-challenge