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R4 and Seurat

Workshop:

  • Date: 10/23/2023

  • Title: Created for the Tools for Single-Cell Genomics Analysis Workshops. Part 1: Single-Cell RNA Sequencing Data Analysis

  • Presenter: Dr Qian-Quan Sun

Environment: Conda environment build with R v4.3.1 and Seurat v4.4.0

This environment can be used on:

  1. SouthPass within a Shell tab.

  2. SouthPass within an interactive desktop (4 cpus and 16G) - this does not require an salloc as the session is already on a compute node.

  3. Beartooth command-line.

How to Use

# Create an interactive session so you're not running on a login node.
[~]$ salloc -A <account> arcc -t <time_required> --mem=16G
# Navigate to location of the R script to run.
[~]$ cd <script_location>
[]$ module load workshop/r4_seurat
[]$ Rscript Rscript <script>.R

You can not use this environment within RStudio via an interactive desktop session on SouthPass.

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