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kappa-casein-evolution-paper

This repository contains the data and code for our paper:

Jean Manguy and Denis C. Shields (2019). Implications of kappa-casein evolutionary diversity for the self-assembly and stabilization of casein micelles. Royal Society Open Science https://doi.org/10.1098/rsos.190939

This repository is archived on Zenodo: DOI: 10.5281/zenodo.2587122

Analysis

The code for the figures and the output can be viewed in a web browser, download and open the file figures_and_tables_paper.html.

We use {ProjectTemplate} to manage the analysis. The code was tested only on Linux.

Install dependencies

  1. download IUPred2A from https://iupred2a.elte.hu/download and unzip the archive in lib/iupred2a/ (non-commercial users only)
  2. install R >= 3.5 and python >= 3
  3. install R packages (see session_info.txt)

Generates the figures only

  1. go to root of this repository
  2. run:
library(ProjectTemplate)
load.project()

Run the rmarkdown file

With Rstudio

  1. open this repository with Rstudio
  2. open figures_and_tables_paper.Rmd from Rstudio
  3. Click on Run > run all (or Ctrl+Alt+R)

Without Rstudio

Run in a unix shell

R -e "rmarkdown::render('figures_and_tables_paper.Rmd')"

Funding

Funded by Enterprise Ireland grants to Food for Health Ireland [TC2013001; TC20180025].