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("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 | ||
| 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 |