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(
    "tidyverse", "SummarizedExperiment", "hexbin",
    "patchwork", "gridExtra", "lubridate",
    "GenomicRanges", "Biostrings"
)

BiocManager::install(packages)

Course materials

Throughout the course, you will use some example data sets. 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/r-bioc-intro
  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?)