EvAM-Tools: tools for evolutionary accumulation and cancer progression models.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36287062.
- Also identified by DOI 10.1093/bioinformatics/btac710 and PMC identifier 9750106.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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 data are available at Bioinformatics online.
Medical subject headings
- Software
- Neoplasms