3  Installations

3.1 Description

This document provides installation guides for basic programming tools.

3.2 R

R is a commonly used coding language for computational biologists and immunologists. Many software packages and analysis pipelines depend on R. R is also a computational environment used for computing and generating graphics.

To install R for Windows or Mac, follow the instructions provided by The Comprehensive R Archive Network (CRAN) found here: https://cran.r-project.org/

It is recommended to download the precompiled binary distribution appropriate for your machine.

To learn more about R, read the following introduction provided by CRAN: https://www.r-project.org/about.html

3.3 R Studio

RStudio is an integrated development environment (IDE) based on R. It provides a user-friendly option for building code and can incorporate multiple languages including python, which is also commonly used by computational immunologists.

To donwload and install RStudio Desktop, follow this link and the provided instructions: https://posit.co/download/rstudio-desktop/#download

3.4 GitHub Desktop

GitHub Desktop is a desktop application that interfaces with version-controlled code, GitHub, and other Git services. It provides a user friendly GUI where you can review changes made to code and perform Git commands. It is open source and free to use.

First sign up for a GitHub account at https://github.com

Now download and install GitHub Desktop, follow this link and the provided instructions: https://desktop.github.com. Sign in with your GitHub account login.

3.5 Visual Studio Code (VS Code)

VS Code is a text and code editor commonly used by developers. It can be used as an alternative for RStudio and supports multiple coding languages and various extensions for debugging and version control.

To download and install VS Code, follow this link and the provided instructions: https://code.visualstudio.com/download