Summary and Setup

This is a new lesson built with The Carpentries Workbench.

This workshop was developed by Luke C. Gandolfo for Melbourne Bioinformatics.

Please follow the steps below and install the required software before the scheduled workshop.

Data Sets

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Data: Obers et al. “Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency”, Immunity (2024)

Download the GSE232852_CountsTable.txt data file and place it in the workshop folder.

RStudio Setup

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We use RStudio for coding in R.

Click here and follow the instructions to install RStudio Desktop in your system.

Discussion

R packages

Most workshops using R will require the installation of specific packages. Make sure to check in advance with the workshop organisers what packages need to be installed.

You can install packages from CRAN using:

R

install.packages("package_name")

If your package is in a different R repository, such as Bioconductor or GitHub, you may need the BiocManager or devtools packages to install them. To install BiocManager:

R

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

For devtools, you can simply do:

R

install.packages("devtools")

You can then install packages directly from GitHub with:

R

devtools::install_github("username/reponame")