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OncoSimulR

This is the development version of OncoSimulR; for the stable release version, see OncoSimulR.

Forward Genetic Simulation of Cancer Progression with Epistasis


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 4.5.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
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_4.5.0.tar.gz
Windows Binary OncoSimulR_4.5.0.zip
macOS Binary (x86_64) OncoSimulR_4.5.0.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/
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