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Analyze copy number data in BRB CGHTools

An additional component of BRB-ArrayTools, namely CGHTools, is a software package designed to analyze array data obtained from Comparative Genomic Hybridization (CGH) studies. CGH data files from different platforms, including Agilent data in .txt format, Illumina data output from GenomeStudio/BeadStudio in .txt format, Affymetrix data in .cn or .cnt format, or other data in .txt file format with all samples in one file or in separate files, can be imported into BRB-CGHTools. Various analysis tools are provided in CGHTools, including Segmentation, Copy number gain/loss analysis, Identifying frequent copy number aberrations using GISTIC, Pathway enrichment analysis, and Integrated analysis of copy number and expression data. In addition, the copy number data can be converted to a BRB-ArrayTools project, where most of the analysis tools included in BRB-ArrayTools, such as class comparison, clustering, and class prediction, can be applied.

Specification of Gain and Loss Calls analysis in BRB CGHTools

A frequency plot shows the frequencies of copy number gains and losses in a set of samples by chromosomal positions.