Chapter 13 Course materials - Software

Installation and account creation for all software will be covered in detail during class or via assignments and accompanying videos. If you want to get prepared early for the course you can explore these on your own.

For information on getting started with R see Get R Done!.

13.1 Primary software

13.1.1 Programming environment: R

We will use the open-source language R for almost everything in this course.

NOTE: If you have used R before that’s awesome!

However, PLEAE PLEASE PLEASE update your installation when the class begins - R goes through regular updates and works best with the newest version.

If you are having trouble installing R an excellent resource is: https://learningstatisticswithr.com/book/introR.html

REFERENCE
R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.R-project.org/.

13.1.2 Integrated developement environment (IDE)

We’ll use RStudio as the front-end for working with R.

NOTE: If you’ve use RStudio before please update it when the course begins.

[RStudio](https://www.rstudio.com/: www.rstudio.com/products/rstudio/download/#download

13.1.3 Cloud-based R

We will use several web-based services to run R. First, we will use the online machine-learning platform Kaggle and the Notebooks feature to run code in a user-friendly environment. You can make a Kaggle account with your University or personal email address.

Additionally, as a back-up to running R on your desktop I’ll also introduce you to [RStudio Cloud](https://rstudio.cloud/. There are also several excellent primers which we’ll use.

RStudio cloud: https://rstudio.cloud/

13.2 R packages

Many R packages (aka libraries) will be used in this course. Below are several key ones.

13.2.1 swirl

swirl is an R package that sets up interactive tutorials in your R console. It works both on desktop computers and RStudio cloud and is an excellent tool for learning and reviewing R.

Details for installing swirl can be found here in Get R Done!.

13.2.2 Bioconductor

Bioconductor is a clearing house and repository for high-grade bioinformatics and computational biology software using R.

Details for installing Bioconductor can be found here.