# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "OncoSimulR" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis'
version: 4.7.3
doi: 10.1093/bioinformatics/btx077
identifiers:
- type: doi
  value: 10.32614/CRAN.package.OncoSimulR
abstract: '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.'
authors:
- family-names: Diaz-Uriarte
  given-names: Ramon
  email: rdiaz02@gmail.com
- family-names: Sanchez-Carrillo
  given-names: Sergio
  email: sergiosanchezcarrillo@gmail.com
- family-names: Miguel Gonzalez
  given-names: Juan Antonio
  email: juanantonio.miguel792@gmail.com
- family-names: Mu~noz Haro
  given-names: Javier
- family-names: Gonzalez Klein
  given-names: Alberto
- family-names: Lopez Cano
  given-names: Javier
preferred-citation:
  type: article
  title: 'OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes
    in asexual populations.'
  authors:
  - family-names: Diaz-Uriarte
    given-names: R
  journal: Bioinformatics
  year: '2017'
  volume: '33'
  issue: '12'
  doi: 10.1093/bioinformatics/btx077
  publisher:
    name: Oxford University Press
  url: https://doi.org/10.1093/bioinformatics/btx077
  start: '1898'
  end: '1899'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/rdiaz02/OncoSimul
commit: d8bc8065ce76cf3b23e65757e45ac42b7b8c063e
url: https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
date-released: '2024-07-26'
contact:
- family-names: Diaz-Uriarte
  given-names: Ramon
  email: rdiaz02@gmail.com
references:
- type: article
  title: Every which way? On predicting tumor evolution using cancer progression models
  authors:
  - family-names: Diaz-Uriarte
    given-names: R
  - family-names: Vasallo
    given-names: C
  journal: PLoS Computational Biology
  year: '2019'
  volume: '15'
  issue: '8'
  doi: 10.1371/journal.pcbi.100724610.1101/371039
  url: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007246
- type: article
  title: 'Cancer progression models and fitness landscapes: a many-to-many relationship'
  authors:
  - family-names: Diaz-Uriarte
    given-names: R
  journal: Bioinformatics
  year: '2018'
  doi: 10.1093/bioinformatics/btx663
  url: https://academic.oup.com/bioinformatics/article/34/5/836/4557185
  volume: '34'
  issue: '5'
  start: '836'
  end: '844'
- type: article
  title: 'Identifying restrictions in the order of accumulation of mutations during
    tumor progression: effects of passengers, evolutionary models, and sampling'
  authors:
  - family-names: Diaz-Uriarte
    given-names: R
  journal: BMC Bioinformatics
  year: '2015'
  doi: 10.1186/s12859-015-0466-7
  url: http://www.biomedcentral.com/1471-2105/16/41/abstract
  volume: '16'
  issue: '41'