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.

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.

Date/Time: 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST

Location: Online

Learning outcomes:

By the end of the workshop you should be able to:

  1. Load gene counts into a Seurat format
  2. Perform QC and select cells for further analysis
  3. Filter and normalise scRNAseq data
  4. Cluster cells and identify cluster markers
  5. 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:

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.

Applications close at 11:59pm AEDT, Wednesday 10 August 2022.

Apply here

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

Start: Monday, 22 August 2022 @ 13:00

End: Tuesday, 23 August 2022 @ 17:00

Timezone: Canberra

Eligibility:
  • Registration of interest

Organizer: Australian BioCommons

Contact: training@biocommons.org.au

Host institutions: Australian Biocommons

Keywords: Single Cell technologies, scRNAseq, Seurat, R software

Capacity: 80

Event type:
  • Workshops and courses

Scientific topics: RNA-Seq

Operations: Visualisation, Analysis