Summary and Schedule

About this course

R is a programming language, an environment for statistical computing, and its a software that interprets the scripts written in R language. It excels at customizable high-quality graphics, statistical computing across many disciplines, and reproducibility.

Please note that these lesson materials were imported and modified from the Carpentries Incubator lesson, bioc-intro, created by a Bioconductor team. The original Carpentries Creative Commons license can be found here. The Carpentries do not endorse HPCBio’s version of this lesson.

Prerequisites

  • Familiarity with tabular data and spreadsheets.

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

  • If you’re planning on learning the optional first episode, please make sure you have a spreadsheet editor at hand, such as LibreOffice, Microsoft Excel or Google Sheets.

  • Install R, RStudio and necessary packages (see below).

R and RStudio

  • R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. After installing both programs, you will need to install some specific R packages within RStudio. Follow the instructions below for your operating system, and then follow the instructions to install packages.

You are running Windows


  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.

  • To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.

  • Follow the steps in the instructions for everyone at the bottom of this page.

  • Download R from the CRAN website.

  • Run the .exe file that was just downloaded

  • Go to the RStudio download page

  • Under All Installers select RStudio xxxx.yy.zz-uuu.exe - Windows 10/11 (where x, y, z, and u represent version numbers)

  • Double click the file to install it

  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages

  • Follow the steps in the instructions for everyone at the bottom of this page.

You are running macOS


  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.

  • To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.

  • Follow the steps in the instructions for everyone at the bottom of this page.

  • Download R from the CRAN website.

  • Select the .pkg file for the latest R version

  • Double click on the downloaded file to install R

  • It is also a good idea to install XQuartz (needed by some packages)

  • Go to the RStudio download page

  • Under All Installers select RStudio xxxx.yy.zz-uuu.dmg - macOS 10.15+ (where x, y, z, and u represent version numbers)

  • Double click the file to install RStudio

  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

  • Follow the steps in the instructions for everyone at the bottom of this page.

You are running Linux


  • Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 4.2.0.
  • Go to the RStudio download page
  • Under All Installers select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb at the terminal).
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.
  • Follow the steps in the instructions for everyone

For everyone

After installing R and RStudio, you need to install a couple of packages that will be used during the workshop. We will also learn about package installation during the course to explain the following commands. For now, simply follow the instructions below:

  • Start RStudio by double-clicking the icon and then type:

R 

install.packages(c("BiocManager", "remotes"))
BiocManager::install(c("tidyverse", "SummarizedExperiment", "hexbin",
                       "patchwork", "gridExtra", "lubridate"))
  • When it asks the following question, just type ‘n’ for no and then hit enter. This will help you avoid package version conflicts.

R 

Update all/some/none? [a/s/n]: 
n

Additional HPCBio Resources

If you are signed up for an HPCBio workshop, you will have additional resources that you can utilize that will be noted throughout the lessons. These resources are listed below. Make sure to confirm that you have access to both of them. If you’re not signed up for an HPCBio workshop, then you will not have permission to access these. See our website for more workshop information here.

  1. Slack Workshop Group: You should have received an email with an invitation to join our HPCBio Workshops Slack page. Here you can ask HPCBio staff questions related to this material under the channel named # intro-linux-swc.
  2. Video Channel: You should have also received an email containing a link to our video playlist. This includes recordings of HPCBio staff teaching this material if you prefer to listen and follow along with these materials rather than read through the lessons on your own.