OncoSimulR

DOI: 10.18129/B9.bioc.OncoSimulR    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see OncoSimulR.

Forward Genetic Simulation of Cancer Progression with Epistasis

Bioconductor version: 3.11

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], Guillermo Gorines Cordero [ctb], Ivan Lorca Alonso [ctb], Francisco Mu\~noz Lopez [ctb], David Roncero Moro\~no [ctb], Alvaro Quevedo [ctb], Pablo Perez [ctb], Cristina Devesa [ctb], Alejandro Herrador [ctb], Holger Froehlich [ctb], Florian Markowetz [ctb], Achim Tresch [ctb], Theresa Niederberger [ctb], Christian Bender [ctb], Matthias Maneck [ctb], Claudio Lottaz [ctb], Tim Beissbarth [ctb]

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	BiologicalQuestion, Software, SomaticMutation
Version	2.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander
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
Links To Me
Build Report

Package Archives

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

Source Package	OncoSimulR_2.18.0.tar.gz
Windows Binary	OncoSimulR_2.18.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	OncoSimulR_2.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OncoSimulR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OncoSimulR
Package Short Url	https://bioconductor.org/packages/OncoSimulR/
Package Downloads Report	Download Stats