WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.

Event description

Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data. 

We will discuss the 'why' behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.

This workshop is presented by the Australian BioCommons, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.

Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza Jimenez

Facilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) Antczak

Infrastructure provision: Uwe Winter

Coordinator: Melissa Burke

Training materials

Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

• Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
• Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
• scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop

Materials shared elsewhere:

This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'

https://swbioinf.github.io/scRNAseqInR_Doco/index.html

Slides used to introduce key topics are available via GitHub

https://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slides

This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.

It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.