Package: OncoSimulR
Type: Package
Title: Forward Genetic Simulation of Cancer Progression with Epistasis
Version: 4.12.0
Date: 2025-06-09
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")
	      )
Author: Ramon Diaz-Uriarte [aut, cre], Sergio Sanchez-Carrillo [aut],
        Juan Antonio Miguel Gonzalez [aut], Alberto Gonzalez Klein
        [aut], Javier Mu\~noz Haro [aut], Javier Lopez Cano [aut],
        Niklas Endres [ctb], Mark Taylor [ctb], Arash Partow [ctb],
        Sophie Brouillet [ctb], Sebastian Matuszewski [ctb], Harry
        Annoni [ctb], Luca Ferretti [ctb], Guillaume Achaz [ctb],
        Tymoteusz Wolodzko [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], Sara
        Dorado Alfaro [ctb], Miguel Hernandez del Valle [ctb], Alvaro
        Huertas Garcia [ctb], Diego Ma\~nanes Cayero [ctb], Alejandro
        Martin Mu\~noz [ctb], Marta Couce Iglesias [ctb], Silvia Garcia
        Cobos [ctb], Carlos Madariaga Aramendi [ctb], Ana Rodriguez
        Ronchel [ctb], Lucia Sanchez Garcia [ctb], Yolanda Benitez
        Quesada [ctb], Asier Fernandez Pato [ctb], Esperanza Lopez
        Lopez [ctb], Alberto Manuel Parra Perez [ctb], Jorge Garcia
        Calleja [ctb], Ana del Ramo Galian [ctb], Alejandro de los
        Reyes Benitez [ctb], Guillermo Garcia Hoyos [ctb], Rosalia
        Palomino Cabrera [ctb], Rafael Barrero Rodriguez [ctb], Silvia
        Talavera Marcos [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. 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
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:20:29 UTC
RemoteUrl: https://github.com/bioc/OncoSimulR
RemoteRef: RELEASE_3_22
RemoteSha: 0528208eb2e1823e0eaf5c4cb7ca09d2740fe5e7
NeedsCompilation: yes
Packaged: 2025-11-11 16:16:36 UTC; root
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 16:25:15 UTC; windows
Archs: x64
