Analysis scripts accompanying Stammnitz et al., 2023

Maximilian Stammnitz, Transmissible Cancer Group, University of Cambridge (2015–2022)

This repository contains custom R scripts which - in conjunction with the associated supplementary files - can be used to replicate the main figures presented in: The evolution of two transmissible cancers in Tasmanian devils (Stammnitz et al. 2023, Science 380:6642).

The scripts are written to run on R version 3.6.3 or later. You should be able to check your current version of R by running the command below:

R --version

The current R version is also shown when opening RStudio or the R Console.

Scripts require the following R packages: readxl, stringr, scales, lubridate, data.table, Biostrings, GenomicRanges, ggplot2, ggmap, rstudioapi, ggsn, circlize, caper, phytools, treeio, ggtree, rectanglePacking

Although care has been taken to make the code distribution-independent, it is possible that some of the scripts only work on Unix/MacOS systems, and may need to be modified in order to run on Windows systems.

For any feedback or requests, please get in touch with me via email: [email protected]