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.
Lead trainers:
Dr Sarah Williams, Senior Bioinformatician, QCIF
Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF
Dr Ahmed Mehdi, Senior Biostatistician, QCIF
Format
This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action.
The training materials used in this workshop are available in Zenodo.
Date/Time: 22 and 23 August 2022, 1:30-5pm AEST/ 1 - 4:30 pm ACST/ 11:30am - 3pm AWST
Location: Online
Learning outcomes:
By the end of the workshop you should be able to:
Load gene counts into a Seurat format
Perform QC and select cells for further analysis
Filter and normalise scRNAseq data
Cluster cells and identify cluster markers
Visualise scRNAseq expression data
Who the workshop is for:
This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered.
This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2).
You should also have basic knowledge of single cell RNA sequencing technology.
How to apply:
Applications closed on Wednesday 10 August 2022.
This workshop is free but participation is subject to application with selection.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons
Cover image: Visualisation of scRNAseq clustering from Analysis, visualization, and integration of spatial datasets with Seurat under MIT licence.