OncoSimulR

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see OncoSimulR.

Forward Genetic Simulation of Cancer Progression with Epistasis


Bioconductor version: 3.10

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. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). 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 Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OncoSimulR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("OncoSimulR")
OncoSimulR: forward genetic simulation in asexual populations with arbitrary epistatic interactions and a focus on modeling tumor progression. HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, Software, SomaticMutation
Version 2.16.1
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>= 3)
Depends R (>= 3.3.0)
Imports Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, nem
System Requirements
URL https://github.com/rdiaz02/OncoSimul https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
Bug Reports https://github.com/rdiaz02/OncoSimul/issues
See More
Suggests BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package OncoSimulR_2.16.1.tar.gz
Windows Binary OncoSimulR_2.16.1.zip
Mac OS X 10.11 (El Capitan) OncoSimulR_2.16.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/OncoSimulR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OncoSimulR
Bioc Package Browser https://code.bioconductor.org/browse/OncoSimulR/
Package Short Url https://bioconductor.org/packages/OncoSimulR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive