Package: OncoSimulR
 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

 Version: 2.18.0

 Date: 2020-04-27

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"),
 	      person("Guillermo", "Gorines Cordero", role = "ctb"),
 	      person("Ivan", "Lorca Alonso", role = "ctb"),
 	      person("Francisco", "Mu~noz Lopez", role = "ctb"),
 	      person("David", "Roncero Moro~no", role = "ctb"),
 	      person("Alvaro" , "Quevedo" , role = "ctb"),
 	      person("Pablo" ,"Perez" , role = "ctb"),
 	      person("Cristina" ,"Devesa" , role = "ctb"),
 	      person("Alejandro", "Herrador" , role = "ctb"),
 	      person("Holger", "Froehlich", role = "ctb"),
 	      person("Florian", "Markowetz", role = "ctb"),
 	      person("Achim", "Tresch", role = "ctb"),
 	      person("Theresa", "Niederberger", role = "ctb"),
 	      person("Christian", "Bender", role = "ctb"),
 	      person("Matthias", "Maneck", role = "ctb"),
 	      person("Claudio", "Lottaz", role = "ctb"),
 	      person("Tim", "Beissbarth", role = "ctb"))

 Author: Ramon Diaz-Uriarte [aut, cre],

 	Mark Taylor [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]

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

 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

     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.

 biocViews: BiologicalQuestion, SomaticMutation
 License: GPL (>= 3)

 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
 BugReports: https://github.com/rdiaz02/OncoSimul/issues

 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

 Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander

 LinkingTo: Rcpp
 VignetteBuilder: knitr