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Package: OncoSimulR
Type: Package
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Title: Forward Genetic Simulation of Cancer Progression with Epistasis
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Version: 2.13.0
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Date: 2018-07-16
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Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
email = "rdiaz02@gmail.com"),
person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
Author: Ramon Diaz-Uriarte [aut, cre],
Mark Taylor [ctb]
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Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
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Description: 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
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multiple genes or modules of genes, including epistasis, order
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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
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use continuous-time models and can include driver and passenger genes
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and modules. Also included are functions for: simulating random DAGs
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of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks,
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and other tumor progression models; plotting and sampling from
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single or multiple realizations of the simulations, including
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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.
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biocViews: BiologicalQuestion, SomaticMutation
License: GPL (>= 3)
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URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
BugReports: https://github.com/rdiaz02/OncoSimul/issues
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Depends: R (>= 3.3.0)
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Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, nem
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Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander
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LinkingTo: Rcpp
VignetteBuilder: knitr
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