scRNA-seq Differential Expression

(Melbourne Bioinformatics, The University of Melbourne)

This workshop aims to equip participants with the necessary knowledge and skills to analyse scRNA-seq data from two experimental groups effectively, enabling them to integrate multiple datasets, extract differentially expressed genes with different approaches. This workshop is designed to build on material covered in the intro to scRNA-seq workshop. Attendees are expected to have a basic understanding and prior experience using standard Seurat processing workflow steps.

• Researchers and scientists in the fields of biology, genetics, bioinformatics, and related disciplines who are interested in or working with scRNA-seq data.
• Students and early-career researchers or graduate students who are new to scRNA-seq data analysis.
• Experienced bioinformaticians or computational biologists who want to expand their knowledge and skills in scRNA-seq data analysis techniques.

By the end of this training, participants will be able to:

• Understand when and how to use various data integration strategies to correct for batch-effects and enable comparative analyses between multiple single-cell datasets from different experimental groups.
• Understand the differences between Seurat’s in build differential expression functions and when to use them: FindMarkers(), FindConservedMarkers(), and FindAllMarkers()
• Learn how to use DE tools meant for bulk data (e.g. DESeq2 and limma) for single cell ‘pseudobulk’ data, and understand why you might choose this approach
• Take advantage of the Seurat R package to perform the analysis, generate plots and interpret the results.

This Free workshop is available to staff and students at The University if Melbourne and its affiliated institutes.

You must register for this event using an affiliated institutional email address or your registration may be cancelled.

Participants must have familiarity with the R programming language and basic familiarity with Seurat scRNA-seq workflow steps.

This is an in person hands-on workshop and attendees must bring their own computers (laptop chargers also recommended). The following is required:

• R and R-Studio installed
• Additionally, please install and test Seurat, SeuratData, DESeq2, and pheatmap. Instructions for this are included at the beginning of the workshop material(available soon).
• Access to internet via uniwireless or Eduroam
• Web browser (Firefox or Chrome recommended)

If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements:

We recommend that following our eventbrite page if you wish to be alerted when we release new workshops for registrations. If you require any further information, please contact Melbourne Bioinformatics at:

[email protected]

This workshop was made possible through the support of the Graduate Researcher Development Grant from the Faculty of Medicine, Dentistry and Health Sciences (MDHS) at the University of Melbourne.

Host or Publisher Melbourne Bioinformatics