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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("OncoSimulR")
In most cases, you don't need to download the package archive at all.
OncoSimulR
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see OncoSimulR.
Forward Genetic Simulation of Cancer Progression with Epistasis
Bioconductor version: 3.4
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 Tress, Conjunctive Bayesian Networks, and other tumor 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 (from within R,
enter citation("OncoSimulR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("OncoSimulR")
Documentation
| HTML | R Script | OncoSimulR: forward genetic simulation in asexual populations with arbitrary epistatic interactions and a focus on modeling tumor progression. |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BiologicalQuestion, Software, SomaticMutation |
| Version | 2.4.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 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 |
| LinkingTo | Rcpp |
| Suggests | BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown |
| 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | OncoSimulR_2.4.0.tar.gz |
| Windows Binary | OncoSimulR_2.4.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | OncoSimulR_2.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/OncoSimulR/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/OncoSimulR/ |
| Package Downloads Report | Download Stats |
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