A package for fast downstream analysis of large array comparative genomic hybridization datasets. VegaMC enables fast and efficient detection of significant recurrent copy number alterations in very large datasets. It is integrated with the output of the common tools that convert allele signal intensities in log R ratio and B allele frequency. VegaMC also enables the detection of loss of heterozigosity and provides in output two web pages allowing a rapid and easy navigation of the aberrant genes. Synthetic data and real datasets are used for quantitative and qualitative evaluation purposes. By exploiting a multichannel segmentation algorithm, this package identifies the driver genes from LRR and BAF observations. It also enables an easy navigation of the results by html pages.