Section: New Software and Platforms

MPAgenomics package for multi-patient analysis of genomic markers

Participants : Quentin Grimonprez, Guillemette Marot, Alain Celisse.

MPAgenomics is an R package for multi-patients analysis of genomics markers. It enables to study several copy number and SNP data profiles at the same time. It offers wrappers from commonly used packages to offer a pipeline for beginners in R. It also proposes a special way of choosing some crucial parameters to change some default values which were not adapted in the original packages. For multi-patients analysis, it wraps some penalized regression methods implemented in HDPenReg.

MPAgenomics is now available on CRAN (http://cran.r-project.org/web/packages/MPAgenomics/index.html ). New segmentation methods were added to MPAgenomics. Maintenance in 2014 concerned bugs correction, documentation updates and code factorization.