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*NOTE: you need to be connected to the QUT network first, either being on campus or connecting remotely via VPN.

Set up your rVDI environment

Now that you’ve connected to an rVDI virtual machine, you’ll need to set it up to:

1. Connect to your home directory on the HPC, so you can access your data files

2. Install R and RStudio for running the Seurat analysis

Connect to your HPC home directory

Installing R and RStudio

Seurat is an R package, so first we need to install R and RStudio on the rVDI machine. You will be copying and pasting script from this workflow into RStudio.

Download and install R, following the default prompts:

Download R-4.3.2 for Windows. The R-project for statistical computing.

Download and install RStudio, following the default prompts:

https://posit.co/download/rstudio-desktop/

1. nfcore/scrnaseq

10x scRNA-Seq data is typically processed using various Cell Ranger software tools. These (and other) tools have been combined in an nfcore Nextflow workflow called scrnaseq.

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