The development of a manuscript investigating the relationship between mRNA 3'UTR motifs effecting half-lives and their modular effects on transcript abundance.
The data and code (including ALL analysis referred to in the paper) required to create the manuscript is included in this GitHub page. The R package Bookdown, created by Yihui Xie, can be used to recreate the manuscript and re-calculate all of the analysis.
git clone <this repo>
open -a RStudio
# In console at the bottom of RStudio
setwd( <local repo address> )
source("./library_setup.R") # check all required libraries are installed
bookdown::render_book("abstract.Rmd") # this will take a little while
# The pdf version of the manuscript will be created in a _book folder.
The way bookdown works is that it runs all the code in all files, catches any code/graphs outputed then inserts it all into one massive latex document. Therefore, all of the text between code chunks is parsed through a latex compiler, so all latex functionality is availiable. There are many good latex tutorials out there but I recommend (this)[https://www.youtube.com/playlist?list=PLnC5h3PY-znyDQKn3knfXfekZLgWyL7QW] YouTube series for beginners, (this)[https://www.overleaf.com/learn/latex/Main_Page] wiki for more details and finally (this)[https://wch.github.io/latexsheet/] cheatsheet to refresh your memory on syntax.
There are five main .Rmd files that hold the chapter text and analysis code;
When adding new lines of code, especially for importing data, remember it will be ran from the home directory (where ever abstract.Rmd) is not where your current *.Rmd is.
Manage citations using (Bibtex)[http://www.bibtex.org/] and the chimeraProject.bib file. Insert citations using [@] where needed.