# Summary and Schedule

## About this course

Setup Instructions | Download files required for the lesson | |

Duration: 00h 00m | 1. Data organisation with spreadsheets | How to organise tabular data? |

Duration: 01h 00m | 2. R and RStudio | What are R and RStudio? |

Duration: 01h 30m | 3. Introduction to R | First commands in R |

Duration: 03h 30m | 4. Starting with data | First data analysis in R |

Duration: 04h 30m | 5. Manipulating and analysing data with dplyr | Data analysis in R using the tidyverse meta-package |

Duration: 07h 00m | 6. Data visualization | Visualization in R |

Duration: 09h 00m | 7. Next steps |
What is a `SummarizedExperiment` ?What is Bioconductor? |

Duration: 10h 30m | Finish |

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

Please make sure you have a spreadsheet editor at hand, such as LibreOffice, Microsoft Excel or Google Sheets.

Install R, RStudio and 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 downloadedGo 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 versionDouble 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"))
```