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

Ramon Diaz-Uriarte1, Pablo Herrera-Nieto1

  • 1Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain.

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Summary

EvAM-Tools offers a unified interface for cancer progression and evolutionary models. This R package and web app facilitate model construction, data generation, and analysis of evolutionary paths and genotype transitions.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Cancer Research

Background:

  • Cancer progression involves complex evolutionary events.
  • Modeling these events is crucial for understanding tumor development.
  • Existing tools may lack a unified interface for various evolutionary models.

Purpose of the Study:

  • To introduce EvAM-Tools, an R package and web application.
  • To provide a unified interface for cancer progression and evolutionary models.
  • To facilitate model construction, data simulation, and analysis of evolutionary paths.

Main Methods:

  • Development of an R package and a web application with a graphical user interface (GUI).
  • Implementation of state-of-the-art cancer progression and event accumulation models.
  • Inclusion of functionalities for model construction (DAGs, hazard matrices), data generation with error, and analysis of transition matrices and path probabilities.

Main Results:

  • EvAM-Tools provides a unified interface for diverse evolutionary models.
  • Users can construct, simulate data from, and analyze cancer progression models.
  • Outputs include fitted models, transition matrices/rates, and evolutionary path probabilities.

Conclusions:

  • EvAM-Tools simplifies the application of advanced evolutionary models in cancer research.
  • The tool supports the generation of synthetic data for model validation.
  • It enhances the analysis of genotype transitions and evolutionary trajectories in cancer.