copy-number-variation

There are 68 repositories under copy-number-variation topic.

  • sigven/pcgr

    Personal Cancer Genome Reporter (PCGR)

    Language:R2562415048

  • 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.

    Language:HTML95412824

  • gavinha/TitanCNA

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

    Language:R9538237

  • imgag/ClinCNV

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

    Language:R8010464

  • Genotek/ClassifyCNV

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

    Language:Python6081213

  • flowhub-team/CNV

    Copy Number Variation

    58100

  • ShixiangWang/DoAbsolute

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

    Language:R3813512

  • Illumina/witty.er

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

    Language:C#30571

  • DKFZ-ODCF/ACEseqWorkflow

    Allele-specific copy number estimation with whole genome sequencing

    Language:R2313410

  • 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:R2281312

  • vicsanga/Postre

    POSTRE: Prediction Of STRuctural variant Effects

    Language:R21321

  • cbg-ethz/SCICoNE

    Single-cell copy number calling and event history reconstruction.

    Language:C++208767

  • caravagnalab/CNAqc

    CNAqc - Copy Number Alteration (CNA) Quality Check package

    Language:R194308

  • oicr-gsi/sequenza

    Workflow for Sequenza, cellularity and ploidy

    Language:R191022

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

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

    Language:Jupyter Notebook19229

  • OpenOmics/genome-seek

    Clinical Whole Genome and Exome Sequencing Pipeline

    Language:Python1812010

  • TimD1/nPoRe

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

    Language:Python18140

  • bio-ontology-research-group/DeepSVP

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

    Language:Python161364

  • cbg-ethz/SCATrEx

    Map single-cell transcriptomes to copy number evolutionary trees.

    Language:Python13331

  • nriddiford/cnvPlotteR

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

    Language:R13203

  • 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:R1140

  • dpastling/plethora

    Copy number estimation of highly duplicated sequences

    Language:Perl102111

  • 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)

    1010124

  • 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:Python9423

  • bihealth/cnvetti

    :tada: CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data

    Language:Rust85100

  • samabs/conliga

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

    Language:C++8401

  • jakob-he/TADA

    TAD-aware annotation of CNVs

    Language:Python7422

  • bernatgel/CopyNumberPlots

    R package to create plots representing copy number data using karyoploteR

    Language:R6272

  • broadinstitute/tangent

    Language:Shell6305

  • piyalkarum/rCNV

    An R package for detecting copy number variants from SNPs data

    Language:R6321

  • 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:R6374

  • VCCRI/ConanVarvar

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

    Language:R6510

  • waldronlab/subtypeHeterogeneity

    Tumor subclonality of expression-based cancer subtypes

    Language:R6731

  • RRafiee/XHMM

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

    Language:Shell5203

  • skoc/bcpm-pfda-challenge

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

    Language:R5400

  • XUKEREN/phd-pipeline

    Some workflows I wrote for my phd projects

    Language:Shell4101