Setup

Here, I will describe everything you need to do before starting the course. Briefly, you will need to:

  1. Install R, RStudio, and required R packages.
  2. Clone the GitHub repository associated with this course.

Software and required packages

To run the code in this book, you will need to install:

  1. R (>=4.2.0): go to the CRAN website, choose your OS (Windows, Linux, or macOS), and follow the installation instructions.

  2. RStudio Desktop: go to the RStudio website and download the installer for your OS.

After installing R and RStudio, you will need to install some required R packages. To do that, open RStudio and execute the code below in your console:

# Install BiocManager
install.packages("BiocManager")

# Use BiocManager to install required packages
packages <- c(
    "SummarizedExperiment",
    "BioNERO", 
    "cageminer",
    "STRINGdb",
    "tidyverse",
    "here",
    "ggraph"
)

BiocManager::install(packages)

Course materials

Throughout the course, you will use some example data sets that I created specifically for this course. You will also need code handouts to use during the live coding sessions.

To get all the materials you will need to:

  1. Navigate to https://github.com/almeidasilvaf/NASB
  2. Clone the repository by clicking Code > Download ZIP
  3. Extract the .zip file
  4. (Optional) Move the folder with all course materials to a directory of your choice in your machine (you don’t want to leave it in Downloads/, right?)