GitHub topics: copy-number-variation

Repositories

YukiZH/SCOIGET

A Tool for Predicting Spatial Tumor Evolution Pattern by Inferring Spatial Copy Number Variation Distributions

Language: Jupyter Notebook - Size: 30.8 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 0

TNTurnerLab/CNPI

Software for Rapid Analyses of Human Copy Number Data

Language: C++ - Size: 106 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 0

nf-core/tumourevo

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Language: Nextflow - Size: 2.48 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 14 - Forks: 5

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.

Language: HTML - Size: 63 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 100 - Forks: 25

gavinha/TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

Language: R - Size: 10.6 MB - Last synced at: 14 days ago - Pushed at: about 4 years ago - Stars: 97 - Forks: 36

piyalkarum/rCNV

An R package for detecting copy number variants from SNPs data

Language: R - Size: 232 MB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 1

caravagnalab/CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

Language: R - Size: 690 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 19 - Forks: 8

Illumina/witty.er

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

Language: C# - Size: 110 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 32 - Forks: 1

ShixiangWang/DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

Language: R - Size: 2.5 MB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 40 - Forks: 13

vicsanga/Postre

POSTRE: Prediction Of STRuctural variant Effects

Language: R - Size: 136 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 21 - Forks: 1

imgag/ClinCNV

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Language: R - Size: 49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 82 - Forks: 4

Katerina10-cloud/CN-aware-DGE

Language: Jupyter Notebook - Size: 261 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

oicr-gsi/sequenza

Workflow for Sequenza, cellularity and ploidy

Language: R - Size: 314 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 19 - Forks: 2

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Language: Perl - Size: 12.7 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 2

OpenOmics/genome-seek

Clinical Whole Genome and Exome Sequencing Pipeline

Language: Python - Size: 849 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 18 - Forks: 11

DKFZ-ODCF/ACEseqWorkflow

Allele-specific copy number estimation with whole genome sequencing

Language: R - Size: 15.5 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 10

jakob-he/TADA

TAD-aware annotation of CNVs

Language: Python - Size: 196 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 2

mskcc/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Language: R - Size: 240 MB - Last synced at: 20 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 0

skoc/bcpm-pfda-challenge

My Solution for PrecisionFDA Brain Cancer Predictive Modeling and Biomarker Discovery Challenge

Language: R - Size: 170 MB - Last synced at: 2 days ago - Pushed at: about 5 years ago - Stars: 5 - Forks: 0

cbg-ethz/SCICoNE

Single-cell copy number calling and event history reconstruction.

Language: C++ - Size: 33.8 MB - Last synced at: 9 months ago - Pushed at: 11 months ago - Stars: 21 - Forks: 7

auroramaurizio/WES_ESOCA

WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication

Language: Python - Size: 69.3 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

broadinstitute/tangent

Language: Shell - Size: 43.8 MB - Last synced at: 15 days ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 5

KrasnitzLab/CNVMetrics

R Package to compare copy number variant (CNV) results from multiple samples/methods

Language: R - Size: 9.04 MB - Last synced at: 17 days ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 2

mk-runner/IhybCNV

IhybCNV: An intra-hybrid approach for CNV detection from next-generation sequencing data

Language: Python - Size: 55.7 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 3 - Forks: 3

jpuntomarcos/CNVbenchmarkeR2 Fork of TranslationalBioinformaticsIGTP/CNVbenchmarkeR

Framework to benchmark germline copy-number variant detection tools from NGS data

Language: R - Size: 299 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

bio-ontology-research-group/DeepSVP

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity

Language: Python - Size: 843 KB - Last synced at: 1 day ago - Pushed at: about 3 years ago - Stars: 16 - Forks: 4

p4rkerw/Wilson_GBio_2024

Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease

Language: R - Size: 4.58 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

cbg-ethz/SCATrEx

Map single-cell transcriptomes to copy number evolutionary trees.

Language: Python - Size: 3.79 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 1

sigven/pcgr

Personal Cancer Genome Reporter (PCGR)

Language: R - Size: 70.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 236 - Forks: 49

algo-cancer/DETOPT

DETOPT is a combinatorial optimization method for DETermining Optimal Placement in Tumor progression history of SNVs from the genomic regions impacted by CNAs using multi-sample bulk DNA sequencing data

Language: Python - Size: 8.63 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

hodgesr2/Pan-Collagan-Ovarian-Cancer-Study-from-TCGA

MSDS Thesis - Pan-Collagen Survival Analysis of CNV in Ovarian Cancer

Language: HTML - Size: 15.6 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Genotek/ClassifyCNV

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

Language: Python - Size: 26.1 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 54 - Forks: 13

nriddiford/cnvPlotteR

Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec

Language: R - Size: 301 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 3

RRafiee/XHMM

eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data

Language: Shell - Size: 13 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 5 - Forks: 3

Zhihan-Leo-Liu/DosaCNV

Deep multiple instance learning model for predicting deletion pathogenicity and gene haploinsufficiency.

Language: R - Size: 24.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

rptashkin/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Language: R - Size: 240 MB - Last synced at: 20 days ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 4

adeschen/CNprep_test Fork of belleau/CNprep_test 📦

CNprep — Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Language: R - Size: 4.7 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

adeschen/CNprep Fork of KrasnitzLab/CNprep

Processing DNA Copy Number (CN) Data for Detection of CN Events

Language: R - Size: 6.48 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

ndbrown6/innovation-lab

MSKCC CMO Innovation Lab

Language: Makefile - Size: 73.8 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

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.

Language: R - Size: 28.3 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 22 - Forks: 12

flowhub-team/CNV

Copy Number Variation

Size: 10.7 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

bernatgel/CopyNumberPlots

R package to create plots representing copy number data using karyoploteR

Language: R - Size: 2.06 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2

VCCRI/ConanVarvar

ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole genome sequencing data

Language: R - Size: 2.55 MB - Last synced at: 10 days ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 0

yenon118/SoybeanMViz 📦

SoybeanMViz: A Toolset for Annotating Promoter and CNV Regions Using Genotypic and Phenotypic Differences

Language: PHP - Size: 5.68 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

mkelly9513/OV-Project-One

Contains the code and scripts used to process and analyze the data for my analysis of super-enhancer function in ovarian cancer cells (OVCAR3) and in patient RNA-seq and Copy Number data from The Cancer Genome Atlas (TCGA). This project was published by Nat. Communications in July 2022. https://doi.org/10.1038/s41467-022-31919-8

Language: Jupyter Notebook - Size: 4.36 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

TimD1/nPoRe

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Language: Python - Size: 493 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 0

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

A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations

Language: Jupyter Notebook - Size: 20.8 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 19 - Forks: 9

adeschen/CNVMetrics Fork of KrasnitzLab/CNVMetrics

R Package to compare copy number variant (CNV) results from multiple samples or methods

Language: R - Size: 8.98 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

samabs/conliga

Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

Language: C++ - Size: 5.1 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 1

morinlab/tools-morinlab

Galaxy Tool Shed repositories maintained and developed by the Morin Lab.

Language: Python - Size: 54.3 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 6

oicr-gsi/cnv-analysis

Language: Java - Size: 1.3 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

KrasnitzLab/CNprep

CNprep Package - Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Language: R - Size: 5.99 MB - Last synced at: 9 days ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

pughlab/VisCapCancer

Tool for calling tumour-specific somatic copy number alterations from targeted sequencing data. This tool is based on the germline copy number variant caller published by Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

Language: R - Size: 25.4 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 3

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

Language: Python - Size: 176 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 3