Abstract
OncoSimulR implements forward-in-time genetic simulations of diallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can be made to differ between genes, and can be affected by (anti)mutator genes. Also available are sampling from single or multiple simulations, including single-cell sampling, plotting the parent-child relationships of the clones and generating and plotting random fitness landscapes.
Availability and implementation Implemented in R and C++, freely available from BioConductor for Linux, Mac, and Windows under the GNU GPL license. Version 2.3.12 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html. GitHub repository at: https://github.com/rdiaz02/OncoSimul.
