EvAM-Tools: tools for evolutionary accumulation and cancer progression models

Abstract

EvAM-Tools is an R package and web application that provides a unified interface to state-of-the-art cancer progression models (CPMs) and, more generally, evolutionary models of event accumulation. The output includes, in addition to the fitted models, the transition (and transition rate) matrices between genotypes and the probabilities of evolutionary paths. Generation of random cancer progression models is also available. Using the GUI in the web application, users can easily construct models (modifying Directed Acyclic Graphs --DAGs-- of restrictions, matrices of mutual hazards, or specifying genotype composition), generate data from them (with user-specified observational/genotyping error), and analyze the data. Availability and ImplementationImplemented in R and C; open source code available under the GNU Affero General Public License v3.0 at https://github.com/rdiaz02/EvAM-Tools. Docker images freely available from https://hub.docker.com/u/rdiaz02. Web app freely accessible at https://iib.uam.es/evamtools. Contactr.diaz@uam.es