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bioRxiv · 10.1101/2020.07.10.198051

SITH: an R package for visualizing and analyzing a spatial model of intratumor heterogeneity

Phillip B. Nicol·Dániel L. Barabási·Amir Asiaee·Kevin R. Coombes
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Abstract

MotivationCancer progression, including the development of intratumor heterogeneity, is inherently a spatial process. Mathematical models of tumor evolution can provide insights into patterns of heterogeneity that can emerge in the presence of spatial growth. SummaryWe develop SITH, an R package that implements a lattice-based stochastic model of tumor growth and mutation. SITH provides 3D interactive visualizations of the simulated tumor and highlights heavily mutated regions. SITH can produce synthetic bulk and single-cell sequencing data sets by sampling from the tumor. The streamlined API will make SITH a useful tool for investigating the relationship between spatial growth and intratumor heterogeneity. Availability and ImplementationSITH is a part of CRAN and can thus be installed by running install.packages("SITH") from the R console. See https://CRAN.R-project.org/package=SITH for the user manual and package vignette.

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Phillip B. Nicol, Dániel L. Barabási, Amir Asiaee, Kevin R. Coombes. 2020-07-12. SITH: an R package for visualizing and analyzing a spatial model of intratumor heterogeneity. https://doi.org/10.1101/2020.07.10.198051

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