Package: OncoSimulR
Type: Package
Title: Forward Genetic Simulation of Cancer Progression with Epistasis
Version: 4.13.1
Date: 2026-01-31
Authors@R: c(
	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
 	   		     email = "rdiaz02@gmail.com"),
              person("Sergio", "Sanchez-Carrillo", role = "aut",
	        email = "sergiosanchezcarrillo@gmail.com"),
              person("Juan Antonio", "Miguel Gonzalez", role = "aut",
	        email = "juanantonio.miguel792@gmail.com"),
              person("Mark", "Taylor", role = "ctb",
	        email = "ningkiling@gmail.com",
		comment = "plot.stream, plot.stacked"),
	      person("Niklas", "Endres", role = "ctb",
	             comment = "vignette examples, freq-dep-fitness time"),
              person("Javier", "Mu~noz Haro", role = "aut",
		comment = "interventions"),
	      person("Alberto", "Gonzalez Klein", role = "aut",
	        comment = "user-specified death rates"),
	      person("Javier", "Lopez Cano", role = "aut",
	        comment = "user-defined variables"),
	      person("Arash", "Partow", role = "ctb", comment = "ExprTk"),
	      person("Sophie", "Brouillet", role = "ctb", comment = "MAGELLAN"),
	      person("Sebastian", "Matuszewski", role = "ctb",
	             comment = "MAGELLAN"),
	      person("Harry", "Annoni", role = "ctb", comment = "MAGELLAN"),
	      person("Luca", "Ferretti", role = "ctb", comment = "MAGELLAN"),
	      person("Guillaume", "Achaz", role = "ctb", comment = "MAGELLAN"),
	      person("Wolodzko", "Tymoteusz", role = "ctb", comment = "multivariate hypergeometric"),
	      person("Guillermo", "Gorines Cordero", role = "ctb",
	             comment = "rfitness"),
	      person("Ivan", "Lorca Alonso", role = "ctb",
	             comment = "rfitness"),
	      person("Francisco", "Mu~noz Lopez", role = "ctb",
	             comment = "rfitness"),
	      person("David", "Roncero Moro~no", role = "ctb",
	             comment = "rfitness"),
	      person("Alvaro" , "Quevedo" , role = "ctb", comment = "rfitness"),
	      person("Pablo" ,"Perez" , role = "ctb", comment = "rfitness"),
	      person("Cristina" ,"Devesa" , role = "ctb", comment = "rfitness"),
	      person("Alejandro", "Herrador" , role = "ctb",
	             comment = "rfitness"),
	      person("Holger", "Froehlich", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Florian", "Markowetz", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Achim", "Tresch", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Theresa", "Niederberger", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Christian", "Bender", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Matthias", "Maneck", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Claudio", "Lottaz", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Tim", "Beissbarth", role = "ctb",
	             comment = "simOGraph (transitive closure)"),
	      person("Sara", "Dorado Alfaro", role = "ctb",
	             comment = "vignette examples"),
	      person("Miguel", "Hernandez del Valle", role = "ctb",
	             comment = "vignette examples"),
	      person("Alvaro", "Huertas Garcia", role = "ctb",
	             comment = "vignette examples"),
	      person("Diego", "Ma~nanes Cayero", role = "ctb",
	             comment = "vignette examples"),
	      person("Alejandro", "Martin Mu~noz", role = "ctb",
	             comment = "vignette examples"),
	      person("Marta", "Couce Iglesias", role = "ctb",
	             comment = "vignette examples"),
	      person("Silvia", "Garcia Cobos", role = "ctb",
	             comment = "vignette examples"),
	      person("Carlos", "Madariaga Aramendi", role = "ctb",
	             comment = "vignette examples"),
	      person("Ana", "Rodriguez Ronchel", role = "ctb",
	             comment = "vignette examples"),
	      person("Lucia", "Sanchez Garcia", role = "ctb",
	             comment = "vignette examples"),
	      person("Yolanda", "Benitez Quesada", role = "ctb",
	             comment = "vignette examples"),
	      person("Asier", "Fernandez Pato", role = "ctb",
	             comment = "vignette examples"),
	      person("Esperanza", "Lopez Lopez", role = "ctb",
	             comment = "vignette examples"),
	      person("Alberto Manuel", "Parra Perez", role = "ctb",
	             comment = "vignette examples"),
	      person("Jorge", "Garcia Calleja", role = "ctb",
	             comment = "vignette examples"),
	      person("Ana", "del Ramo Galian", role = "ctb",
	             comment = "vignette examples"),
	      person("Alejandro", "de los Reyes Benitez", role = "ctb",
	             comment = "vignette examples"),
	      person("Guillermo", "Garcia Hoyos", role = "ctb",
	             comment = "vignette examples"),
	      person("Rosalia", "Palomino Cabrera", role = "ctb",
	             comment = "vignette examples"),
	      person("Rafael", "Barrero Rodriguez", role = "ctb",
	             comment = "vignette examples"),
	      person("Silvia", "Talavera Marcos", role = "ctb",
	             comment = "vignette examples")
	      )
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. Fitness (including just birth, just death, or
        both birth and death) can also be a function of the relative
        and absolute frequencies of other genotypes (i.e.,
        frequency-dependent fitness). Mutation rates can differ between
        genes, and we can include mutator/antimutator genes (to model
        mutator phenotypes). Simulating multi-species scenarios and
        therapeutic interventions, including adaptive therapy, is also
        possible. 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, additive, NK, Ising, and Eggbox 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 (>= 3.5.0)
Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
        gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
        smatr, ggplot2, ggrepel, stringr
Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
        bookdown, pander
LinkingTo: Rcpp
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-01-31 14:01:26 UTC
RemoteUrl: https://github.com/bioc/OncoSimulR
RemoteRef: HEAD
RemoteSha: 10bf41e6db8a8af90e36613194298efdc238f5ec
NeedsCompilation: yes
Packaged: 2026-02-01 04:35:56 UTC; root
Author: Ramon Diaz-Uriarte [aut, cre],
  Sergio Sanchez-Carrillo [aut],
  Juan Antonio Miguel Gonzalez [aut],
  Mark Taylor [ctb] (plot.stream, plot.stacked),
  Niklas Endres [ctb] (vignette examples, freq-dep-fitness time),
  Javier Mu~noz Haro [aut] (interventions),
  Alberto Gonzalez Klein [aut] (user-specified death rates),
  Javier Lopez Cano [aut] (user-defined variables),
  Arash Partow [ctb] (ExprTk),
  Sophie Brouillet [ctb] (MAGELLAN),
  Sebastian Matuszewski [ctb] (MAGELLAN),
  Harry Annoni [ctb] (MAGELLAN),
  Luca Ferretti [ctb] (MAGELLAN),
  Guillaume Achaz [ctb] (MAGELLAN),
  Wolodzko Tymoteusz [ctb] (multivariate hypergeometric),
  Guillermo Gorines Cordero [ctb] (rfitness),
  Ivan Lorca Alonso [ctb] (rfitness),
  Francisco Mu~noz Lopez [ctb] (rfitness),
  David Roncero Moro~no [ctb] (rfitness),
  Alvaro Quevedo [ctb] (rfitness),
  Pablo Perez [ctb] (rfitness),
  Cristina Devesa [ctb] (rfitness),
  Alejandro Herrador [ctb] (rfitness),
  Holger Froehlich [ctb] (simOGraph (transitive closure)),
  Florian Markowetz [ctb] (simOGraph (transitive closure)),
  Achim Tresch [ctb] (simOGraph (transitive closure)),
  Theresa Niederberger [ctb] (simOGraph (transitive closure)),
  Christian Bender [ctb] (simOGraph (transitive closure)),
  Matthias Maneck [ctb] (simOGraph (transitive closure)),
  Claudio Lottaz [ctb] (simOGraph (transitive closure)),
  Tim Beissbarth [ctb] (simOGraph (transitive closure)),
  Sara Dorado Alfaro [ctb] (vignette examples),
  Miguel Hernandez del Valle [ctb] (vignette examples),
  Alvaro Huertas Garcia [ctb] (vignette examples),
  Diego Ma~nanes Cayero [ctb] (vignette examples),
  Alejandro Martin Mu~noz [ctb] (vignette examples),
  Marta Couce Iglesias [ctb] (vignette examples),
  Silvia Garcia Cobos [ctb] (vignette examples),
  Carlos Madariaga Aramendi [ctb] (vignette examples),
  Ana Rodriguez Ronchel [ctb] (vignette examples),
  Lucia Sanchez Garcia [ctb] (vignette examples),
  Yolanda Benitez Quesada [ctb] (vignette examples),
  Asier Fernandez Pato [ctb] (vignette examples),
  Esperanza Lopez Lopez [ctb] (vignette examples),
  Alberto Manuel Parra Perez [ctb] (vignette examples),
  Jorge Garcia Calleja [ctb] (vignette examples),
  Ana del Ramo Galian [ctb] (vignette examples),
  Alejandro de los Reyes Benitez [ctb] (vignette examples),
  Guillermo Garcia Hoyos [ctb] (vignette examples),
  Rosalia Palomino Cabrera [ctb] (vignette examples),
  Rafael Barrero Rodriguez [ctb] (vignette examples),
  Silvia Talavera Marcos [ctb] (vignette examples)
Built: R 4.6.0; x86_64-w64-mingw32; 2026-02-01 04:38:46 UTC; windows
Archs: x64
