Work

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution

Year: 2017

Type: article

Abstract: SUMMARY: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own. AVAILABILITY AND IMPLEMENTATION: SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: [email protected].

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btx146

Authors: Thomas O McDonald, Franziska Michor

Institutions: Harvard University, Dana-Farber Cancer Institute, Dana-Farber/Harvard Cancer Center

Language: English

Topic: Cancer Genomics and Diagnostics

Subfield: Cancer Research

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Cancer Institute

Award: Evolution and Treatment Response of Brain, Breast, and Hematologic Malignancies