Package creation

This package was created to document and organize the functions that were previously sourced at the start of each script in our workflows. The code was kept almost entirely as is, so that there is very little risk of breaking existing scripts, and it was developed by Holger and Lena - I wrapped it in a package and documented it.

Some changes / notes:

• I also also added .onLoad() and .onAttach() functions to set options and load packages automatically
• The package dependencies were kept at a minimum, but it will attempt to install / load all the packages we need - this was already done silently when sourcing the R helpers.