EvAM-Tools: tools for evolutionary accumulation and cancer progression models.
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ABSTRACT: Summary
EvAM-Tools is an R package and web application that provides a unified interface to state-of-the-art cancer progression models 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 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 implementation
Implemented 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.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Diaz-Uriarte R
PROVIDER: S-EPMC9750106 | biostudies-literature | 2022 Dec
REPOSITORIES: biostudies-literature
Publications
EvAM-Tools: tools for evolutionary accumulation and cancer progression models.
Diaz-Uriarte Ramon R Herrera-Nieto Pablo P
Bioinformatics (Oxford, England) 20221201 24
<h4>Summary</h4>EvAM-Tools is an R package and web application that provides a unified interface to state-of-the-art cancer progression models 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 construc ...[more]
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