Introducing AmplificationTimeR

The Wedge group is excited to announce the publication of AmplificationTimeR a new tool for timing individual copy number gains in cancer genomes. The manuscript is available in full from Bioinformatics.

AmplificationTimeR makes use of copy number calls from Battenberg, multiplicity information from DPClust preprocessing, and a list of mutations to time individual gain or whole genome duplication events affecting segments of the genome that have been gained many times.

The work underpinning AmplificationTimeR originally started out as a side project to investigate the occurrence of MYC gains over time. When it became clear that existing tools for timing copy number gains were not quite suited to the task at hand we decided to develop AmplificationTimeR into a publicly available R package. The Wedge group software engineering sessions led by Julio César Cortés Ríos were pivotal in shaping the structure, development, and testing of the tool.

If you’re interested in using AmplificationTimeR in your work, it can be found on the Wedge group’s GitHub page at https://github.com/Wedge-lab/AmplificationTimeR/. Please share your feedback with us through the Issues page in the tool’s repository. While there are no doubt many improvements that can be made, it has been gratifying to watch AmplificationTimeR progress from an idea, to a side project, to a fully formed R package and publication.