In this repo you find the scripts that produced the results and figures of the gene family evolution analysis from the OneKP capstone paper, as well as the validation of the approach.
This repo contains large files that are stored with git-lfs. You need to install git-lfs before cloning so the large files will automatically be downloaded. Please also see this Stack Overflow question.
First, you can install all programms and packages needed via conda (installation instructions for conda).
conda env create -f conda_env.yml
source activate onekp-gf-evo
Then you can run the main analysis from the paper by starting R and running
source("analysis.r")
To run the two validations uncomment the respective studies in the analysis.r script and rerun th above command. Finally, run the two other r-scripts
source("angiosperm_bias.r")
source("validation_on_model_organisms.R")