Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain.
Bioinformatics. 2022 Dec 13;38(24):5457-5459. doi: 10.1093/bioinformatics/btac710.
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.
EvAM-Tools 是一个 R 包和网络应用程序，为最先进的癌症进展模型提供了一个统一的接口，更广泛地说，为事件积累的进化模型提供了一个统一的接口。除了拟合模型外，输出还包括基因型之间的转移（和转移率）矩阵以及进化路径的概率。还可以生成随机癌症进展模型。用户可以使用网络应用程序中的 GUI 轻松构建模型（修改限制的有向无环图、互风险矩阵或指定基因型组成），从模型中生成数据（具有用户指定的观察/基因分型误差）并分析数据。
用 R 和 C 实现；在 GNU Affero General Public License v3.0 下可从 https://github.com/rdiaz02/EvAM-Tools 获得开源代码。可从 https://hub.docker.com/u/rdiaz02 获得免费的 Docker 映像。网络应用程序可免费访问 https://iib.uam.es/evamtools。
补充数据可在 Bioinformatics 在线获得。
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