An overview of the copynumber package. Depending on the aim of the analysis, the input will be copy number data and possibly allele frequencies from one or more experiments. Preprocessing tools are available for outlier handling and missing data imputation, and three different methods handle single sample, multi-sample and allele-specific segmentation. Several options are also available for the graphical visualization of data and segmentation results.
Nilsen et al. BMC Genomics 2012 13:591 doi:10.1186/1471-2164-13-591