ArticleBioinformatics (Oxford, England)2022
EvAM-Tools: tools for evolutionary accumulation and cancer progression models.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Evolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniae.PLoS biology · 2026Article
- Review
- A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling.Bioinformatics (Oxford, England) · 2024Article
- HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures.PLoS computational biology · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
summaryEvAM-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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.