OncoSimulR

DOI: 10.18129/B9.bioc.OncoSimulR    

Forward Genetic Simulation of Cancer Progression with Epistasis

Bioconductor version: Release (3.12)

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 (from 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], Mark Taylor [ctb], Arash Partow [ctb], Sophie Brouillet [ctb], Sebastian Matuszewski [ctb], Harry Annoni [ctb], Luca Ferretti [ctb], Guillaume Achaz [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], Niklas Endres [ctb]

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

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

Installation

To install this package, start R (version "4.0") 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 2.20.0
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_2.20.0.tar.gz
Windows Binary OncoSimulR_2.20.0.zip
macOS 10.13 (High Sierra) OncoSimulR_2.20.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: