Prerequisites

Minimum System Requirements

  • OS: Windows 10/11

  • Memory: > 8 GB RAM

  • ROM: storage using Solid-state drive (SSD) is preferable. (Here’s how to check)

  • OS: macOS 11 (Big Sur) or higher

  • Memory: > 8 GB RAM

Software Requirements

Before the workshop day, users are asked to install the following software in advance.

1. Install R

R is programming language for statistical computing and graphical visualization, and is an open-source software for computing in R language.

Users can download R installer from the Comprehensive R Archive Network (CRAN): https://cran.rstudio.com.

The latest R version is 4.3.0 (2023-04-21) -- "Already Tomorrow".

2. Install Rtools (Windows users only)

Rtools is used to build and install R packages from source code. Some important tools, such as tidyverse, require Rtools to install on Windows.

Users can install Rtools from CRAN: https://cran.rstudio.com/bin/windows/Rtools/rtools43/files/rtools43-5550-5548.exe

The current Rtools for Windows users is Rtools 4.3, which is compatible with version R 4.3.x.

3. Install Rstudio Desktop

Rstudio is an integrated development environment (IDE) for computing in R language. Users can install Rstudio Desktop from official posit website https://posit.co/download/rstudio-desktop.

Current Rstudio Desktop version is Released: 2023-05-12.

4. Install necessary R packages

Participants are required to install the following R packages from 2 sources, CRAN and Bioconductor, before the workshop day. All packages can be installed by copy and paste the following commands to RStudio console panel (in the bottom left panel of the RStudio screen), and hit the Enter key. Make sure your computer is already connected to the Internet.

Copy and paste the installation commands to the console.

4.1 Install packages from CRAN:

if (!require("pacman"))
  install.packages("pacman"
  )
pacman::p_load(
  tidyverse,
  paletteer,
  scales,
  RColorBrewer,
  ggpubr,
  VennDiagram,
  circlize,
  viridis,
  png,
  GGally,
  cowplot,
  openxlsx,
  gridExtra,
  gtable,
  egg,
  ggfortify,
  FactoMineR,
  factoextra,
  gridGraphics,
  corrplot,
  plotly,
  agricolae,
  ggsci
)

Copy and paste the installation commands to the console.

4.2 Install packages from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install(c("ComplexHeatmap", "DESeq2", 
                       "pcaExplorer", "EnhancedVolcano"))

📧 For technical issues regarding R packages installation, please email the issues to Prasert Yodsawat (prasert.y@outlook.com).

Optional 📖

In addition, users with some experience with R are beneficial. This workshop focuses on intermediate knowledge of R for managing and visualizing data. We recommend that participants familiarize themselves with the basics of R before attending this workshop. Here we also provide some online courses that would be helpful: