| 2f97de14 | Package: OncoSimulR Type: Package |
| 5a471d04 | Title: Forward Genetic Simulation of Cancer Progression with Epistasis |
| 17fdf397 | Version: 3.4.0 |
| 41274357 | Date: 2021-10-06 |
| f4821fe3 | 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("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("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"),
person("Niklas", "Endres", role = "ctb",
comment = "vignette examples, freq-dep-fitness time")
)
|
| debcf5f5 | Author: Ramon Diaz-Uriarte [aut, cre], |
| f4821fe3 | Sergio Sanchez-Carrillo [aut], Juan Antonio Miguel Gonzalez [aut], |
| eb537117 | Mark Taylor [ctb], |
| f4821fe3 | Arash Partow [ctb], Sophie Brouillet [ctb], Sebastian Matuszewski [ctb], Harry Annoni [ctb], Luca Ferretti [ctb], Guillaume Achaz [ctb], |
| eb537117 | 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], |
| f4821fe3 | 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], |
| 4068375e | Niklas Endres [ctb] |
| 2f97de14 | Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com> |
| e693f153 | 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
|
| 5d9775a3 | multiple genes or modules of genes, including epistasis, order |
| 4068375e | restrictions in mutation accumulation, and order effects. Fitness 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 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.
|
| 2f97de14 | biocViews: BiologicalQuestion, SomaticMutation License: GPL (>= 3) |
| e6e95f54 | URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/ BugReports: https://github.com/rdiaz02/OncoSimul/issues |
| 4068375e | 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 |
| bbd76086 | Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander |
| 2f97de14 | LinkingTo: Rcpp VignetteBuilder: knitr |
| 5d9775a3 |