R Workshop Environments

Owned by Simon Alexander
Last updated: Oct 19, 2023
1 min read

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. Beartooth command-line terminal.

  2. SouthPass within a Shell tab.

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

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

How to Use

From a terminal:

# 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

From a SouthPass interactive desktop (4 cpus and 16G) running R:tudio

# Start an interactive desktop session. # Open a terminal. []$ module load workshop/r4_seurat []$ module load rstudio/2023.9.0 []$ rstudio