R-based Workshop Specifications

Modified

July 1, 2026

This page outlines the software requirements and specifications for R-based workshops.

Fully R/RStudio based workshops:

All packages needed across these workshops:

install.packages("tidyverse")
install.packages("palmerpenguins")
install.packages("viridis")
install.packages("devtools")
devtools::install_github("G-Thomson/Manu")
install.packages("scales")
install.packages("ggbeeswarm")
install.packages("ggridges")
install.packages("vegan")

Load libraries:

library(tidyverse)
library(palmerpenguins)
library(viridis)
library(devtools)
library(Manu)
library(scales)
library(ggbeeswarm)
library(ggridges)
library(vegan)

Individual workshop set-up

Introduction to R

GitHub : https://github.com/GenomicsAotearoa/Introduction-to-R

General description: This workshop uses primarily base R tools and default packages installed in RStudio. It uses one example dataset, which needs to be pre-loaded on the REANNZ training environment in R4Genomics dir, but there is also a direct github link included in the material. Only one additional library is needed, which is ggplot2.

Packages/libraries

install.packages("ggplot2")
library(ggplot2)

Dataset

Load in R:

variants <- read.csv("https://raw.githubusercontent.com/GenomicsAotearoa/Introduction-to-R/refs/heads/main/combined_tidy_vcf.csv")

 

Visualisation with ggplot2

GitHub : https://github.com/GenomicsAotearoa/visualization_day

General description: This workshop uses tidyverse tools and some extra packages for colours and geoms. It uses one example dataset, which is not pre-loaded on the REANNZ training environment and is supplied in the material as a direct github link. Many tidyverse tools are needed in this workshop (ggplot2, dplyr, lubridate, forcats etc) so we recommend installing all tidyverse.

Packages/libraries

install.packages("tidyverse")
install.packages("palmerpenguins")
install.packages("viridis")
install.packages("devtools")
devtools::install_github("G-Thomson/Manu")
install.packages("scales")
install.packages("ggbeeswarm")
install.packages("ggridges")
library(tidyverse)
library(palmerpenguins)
library(viridis)
library(Manu)
library(scales)
library(ggbeeswarm)
library(ggridges)
library(glue)

Dataset

Load in R:

top_group_counts <- read.delim("https://raw.githubusercontent.com/GenomicsAotearoa/visualization_day/refs/heads/main/data/eDNA_group_counts.tsv")


Intermediate R for bioinformatics

GitHub : https://github.com/GenomicsAotearoa/Intermediate-R

General description: This workshop uses multiple tidyverse tools and vegan, in addition to base R/default RStudio packages. It uses three example datasets, which are not pre-loaded on the REANNZ training environment and are supplied in the material as direct github links.

Packages/libraries

install.packages("tidyverse")
install.packages("vegan")
library(tidyverse)
library(vegan)

Dataset

Load in R:

asv <- read.delim("https://raw.githubusercontent.com/GenomicsAotearoa/Intermediate-R/main/tables/asv_table.tsv")
env <- read.delim("https://raw.githubusercontent.com/GenomicsAotearoa/Intermediate-R/main/tables/env_table.tsv")
tax <- read.delim("https://raw.githubusercontent.com/GenomicsAotearoa/Intermediate-R/main/tables/taxonomy.tsv")

 

WORK IN PROGRESS…

Partially R/RStudio based workshops

install.packages("tidyverse")
install.packages("BiocManager")

BiocManager::install("limma")
BiocManager::install("edgeR")
BiocManager::install("DESeq2")
BiocManager::install("gplots")
BiocManager::install("goseq")
install.packages("ggiraph")
install.packages("plotly")
library(tidyverse)
library(limma)
library(edgeR)
library(DESeq2)
library(ggiraph)
library(plotly)
library(gplots)
library(goseq)