Inference of copy number and mutation multiplicity in oncology
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Updated
May 27, 2024 - R
Inference of copy number and mutation multiplicity in oncology
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.
Framework to benchmark germline copy-number variant detection tools from NGS data
Single-cell copy number calling and event history reconstruction.
Personal Cancer Genome Reporter (PCGR)
Clinical Whole Genome and Exome Sequencing Pipeline
An R package for detecting copy number variants from SNPs data
Map single-cell transcriptomes to copy number evolutionary trees.
IhybCNV: An intra-hybrid approach for CNV detection from next-generation sequencing data
CNAqc - Copy Number Alteration (CNA) Quality Check package
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package
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
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Allele-specific copy number estimation with whole genome sequencing
Workflow for Sequenza, cellularity and ploidy
Deep multiple instance learning model for predicting deletion pathogenicity and gene haploinsufficiency.
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