This repository contains the scripts used in "Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups" (Rueda OM, Sammut SJ, Seoane JA, Chin SF, Caswell-Jin JL, Callari M, Batra R, Pereira B, Bruna A, Ali HR, Provenzano E, Liu B, Parisien M, Gillett C, McKinney S, Green AR, Murphy L, Purushotham A, Ellis IO, Pharoah PD, Rueda C, Aparicio S, Caldas C, Curtis C. Nature. 2019 Mar 13. doi: 10.1038/s41586-019-1007-8) It will be updated with new material or new software versions.