Comprehensive Pipeline for Analyzing and Visualizing Agilent
and Affymetrix Array-Based CGH Data
Description
A comprehensive pipeline for analyzing and interactively
visualizing genomic profiles generated through Agilent and Affymetrix
microarrays. As inputs, rCGH supports Agilent dual-color Feature Extraction
files (.txt), from 44 to 400K, and Affymetrix SNP6.0 and cytoScan
probeset.txt, cychp.txt, and cnchp.txt files, exported from ChAS or
Affymetrix Power Tools. This package takes over all the steps required for
a genomic profile analysis, from reading the files to the segmentation and
genes annotations, and provides several visualization functions (static or
interactive) which facilitate profiles interpretation.
Input files can be in compressed format, e.g. .bz2 or .gz.