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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see OncoSimulR.

Forward Genetic Simulation of Cancer Progresion with Epistasis

Bioconductor version: 3.3

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models, and for plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling, as well as functions for plotting the true phylogenetic relationships of the clones.

Author: Ramon Diaz-Uriarte [aut, cre], Mark Taylor [ctb]

Maintainer: Ramon Diaz-Uriarte <rdiaz02 at>

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PDF R Script OncoSimulR Overview
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biocViews BiologicalQuestion, Software, SomaticMutation
Version 2.2.2
In Bioconductor since BioC 3.0 (R-3.1) (2 years)
License GPL (>= 3)
Depends R (>= 3.1.0)
Imports Rcpp (>= 0.11.1), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices
LinkingTo Rcpp
Suggests BiocStyle, knitr, Oncotree, testthat
Depends On Me
Imports Me
Suggests Me
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