OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations

Bioinformatics. 2017 Jun 15;33(12):1898-1899. doi: 10.1093/bioinformatics/btx077.

Abstract

Summary: 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.

Availability and implementation: 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.

Contact: ramon.diaz@iib.uam.es.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Computational Biology / methods*
  • Computer Simulation
  • Epistasis, Genetic*
  • Mutation*
  • Neoplasms / genetics
  • Single-Cell Analysis / methods
  • Software*