To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

OncoSimulR

   

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 gmail.com>

Citation (from within R, enter citation("OncoSimulR")):

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")

 

PDF R Script OncoSimulR Overview
PDF   Reference Manual
Text   NEWS

Details

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
SystemRequirements
Enhances
URL https://github.com/rdiaz02/OncoSimul https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
BugReports https://github.com/rdiaz02/OncoSimul/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source OncoSimulR_2.2.2.tar.gz
Windows Binary OncoSimulR_2.2.2.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) OncoSimulR_2.2.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/OncoSimulR/tree/release-3.3
Package Short Url http://bioconductor.org/packages/OncoSimulR/
Package Downloads Report Download Stats

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