OncoSimulR

DOI: 10.18129/B9.bioc.OncoSimulR  

Forward Genetic Simulation of Cancer Progression with Epistasis

Bioconductor version: Release (3.17)

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. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. 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, additive, NK, Ising, and Eggbox models) and plotting them.

Author: Ramon Diaz-Uriarte [aut, cre], Sergio Sanchez-Carrillo [aut], Juan Antonio Miguel Gonzalez [aut], Alberto Gonzalez Klein [aut], Javier Mu\~noz Haro [aut], Javier Lopez Cano [aut], Niklas Endres [ctb], Mark Taylor [ctb], Arash Partow [ctb], Sophie Brouillet [ctb], Sebastian Matuszewski [ctb], Harry Annoni [ctb], Luca Ferretti [ctb], Guillaume Achaz [ctb], Tymoteusz Wolodzko [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], Sara Dorado Alfaro [ctb], Miguel Hernandez del Valle [ctb], Alvaro Huertas Garcia [ctb], Diego Ma\~nanes Cayero [ctb], Alejandro Martin Mu\~noz [ctb], Marta Couce Iglesias [ctb], Silvia Garcia Cobos [ctb], Carlos Madariaga Aramendi [ctb], Ana Rodriguez Ronchel [ctb], Lucia Sanchez Garcia [ctb], Yolanda Benitez Quesada [ctb], Asier Fernandez Pato [ctb], Esperanza Lopez Lopez [ctb], Alberto Manuel Parra Perez [ctb], Jorge Garcia Calleja [ctb], Ana del Ramo Galian [ctb], Alejandro de los Reyes Benitez [ctb], Guillermo Garcia Hoyos [ctb], Rosalia Palomino Cabrera [ctb], Rafael Barrero Rodriguez [ctb], Silvia Talavera Marcos [ctb]

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

Installation

To install this package, start R (version "4.3") 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")

 

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	4.2.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	GPL (>= 3)
Depends	R (>= 3.5.0)
Imports	Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr
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
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Build Report

Package Archives

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

Source Package	OncoSimulR_4.2.0.tar.gz
Windows Binary	OncoSimulR_4.2.0.zip
macOS Binary (x86_64)	OncoSimulR_4.2.0.tgz
macOS Binary (arm64)
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 3.17	Source Archive