title: OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.
abstract: CONCLUSIONS
  OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes.
  
  
  METHODS
  Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul.
  
  
  BACKGROUND
  ramon.diaz@iib.uam.es.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas 'Alberto Sols' (UAM-CSIC), Madrid, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Diaz-Uriarte
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004843:Epistasis, Genetic; D009154:Mutation; D009369:Neoplasms / Q000235:genetics; D059010:Single-Cell Analysis / Q000379:methods; D012984:Software