OncoSimulR

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see OncoSimulR.

Forward Genetic Simulation of Cancer Progresion with Epistasis

Bioconductor version: 3.2

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.

Maintainer: Ramon Diaz-Uriarte <rdiaz02 at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("OncoSimulR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OncoSimulR")

Details

Package Archives

Follow Installation instructions to use this package in your R session.