Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils - supporting code

This repository contains code required to reproduce figures and analysis in the paper "Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils".

Installation

The most direct way to get this repository onto your computer is using git:

git clone --recursive https://github.com/TransmissibleCancerGroup/TCG_2020_devil_paper.git

The --recursive flag is there so that the submodules dftdLowCov and additional_scripts will be downloaded all in one go. If --recursive is left out, it is still possible to get the submodules by using the command git submodule update --init --recursive.

R package

Some of the code relies on dftdLowCov being installed as an R package. This can be done from an R terminal using the package devtools.

Install from the remote repository

# Inside an R terminal...
require(devtools)
devtools::install_git(
    "https://github.com/TransmissibleCancerGroup/TCG_2020_devil_paper.git",
    subdir = "dftdLowCov",
    args = "--recursive")

Install from a local copy of the repository

# Inside an R terminal...
require(devtools)
devtools::install_local("/path/to/dftdLowCov")  # replace with actual path