The tool quandico applies statistical methods to detect copy number variations (CNV) in a sample by comparing the read counts from next generation sequencing (NGS) performed after PCR-enrichment of regions of interest, typically a set of genes with known or expected relevance for the sample, e.g. genes that play a role in cancer. Counts from a normal control (ideally matched normal from the same individual, e.g. healthy tissue) are required.
CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data
CoNCoS is a tool for researchers concerned with copy number estimation from next-generation sequencing data.It detects copy number aberrations and outputs a list composed of their position, copy number and affected gene(s).
CopyNumber450kCancer takes the output of CopyNumber450k and ChAMP packages and correct the baseline in each sample for accurate copy number calling, specially in cancer samples. CopyNumber450kCancer can read the segment output file from CopyNumber450k package directly without any need for modification. Output files from ChAMP need to be in one file not in seperated files.
The jointSeg R package implements functions to quickly segment multivariate signals into piecewise constant profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies.