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Introduction
Introduction to the Workshop and the Core
Course Materials
Prepare R and RStudio
Introduction to ggplot2 and box plots
Scatter plots
Bar plots
Advanced plotting
ETC
Github page
Biocore website

For this course, you will need an up-to-date version of R (4.4.0 or higher) and RStudio. In the course of the workshop, we will be using a number of packages. Let’s get them all installed before we start.

Set up and installations

BiocManager

if (!any(rownames(installed.packages()) == "BiocManager")){
  install.packages("BiocManager")
}

Rmarkdown

if (!any(rownames(installed.packages()) == "Rmarkdown")){
  BiocManager::install("Rmarkdown")
}

Cleaning and managing data

dplyr

if (!any(rownames(installed.packages()) == "dplyr")){
  BiocManager::install("dplyr")
}

tidyr

if (!any(rownames(installed.packages()) == "tidyr")){
  BiocManager::install("tidyr")
}

magrittr

if (!any(rownames(installed.packages()) == "magrittr")){
  BiocManager::install("magrittr")
}

kableExtra

if (!any(rownames(installed.packages()) == "kableExtra")){
  BiocManager::install("kableExtra")
}

Basic visualizations

ggplot2

if (!any(rownames(installed.packages()) == "ggplot2")){
  BiocManager::install("ggplot2")
}

ggExtra

if (!any(rownames(installed.packages()) == "ggExtra")){
  BiocManager::install("ggExtra")
}

ggsignif

if (!any(rownames(installed.packages()) == "ggsignif")){
  BiocManager::install("ggsignif")
}

ggrepel

if (!any(rownames(installed.packages()) == "ggrepel")){
  BiocManager::install("ggrepel")
}

ggalluvial

if (!any(rownames(installed.packages()) == "ggalluvial")){
  BiocManager::install("ggalluvial")
}

Advanced visualizations

circlize

if (!any(rownames(installed.packages()) == "circlize")){
  BiocManager::install("circlize")
}

ggtree

if (!any(rownames(installed.packages()) == "ggtree")){
  BiocManager::install("ggtree")
}

ggcoverage

if (!any(rownames(installed.packages()) == "ggcoverage")){
  install.package("remotes")
  remotes::install_github("showteeth/ggcoverage")
}

Complex Heatmap

if (!any(rownames(installed.packages()) == "ComplexHeatmap")){
  BiocManager::install("ComplexHeatmap")
}

Download markdown documentation

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2025-August-Intermediate-Visualization-for-Bioinformatics/R/01-boxplot.Rmd")

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Introduction to R for Bioinformatics