Thomas O McDonald1, Franziska Michor1. 1. Department of Biostatistics and Computational Biology, Center for Cancer Evolution, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
Abstract
SUMMARY: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own. AVAILABILITY AND IMPLEMENTATION: SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: michor@jimmy.harvard.edu.
SUMMARY: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own. AVAILABILITY AND IMPLEMENTATION: SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: michor@jimmy.harvard.edu.
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