Workshop at ABACBS 2023 Brisbane presented by WEHI/SAiGENCI

Interested in learning how to analyze spatial data from NanoString's GeoMX?

Dr Chin Wee Tan and Ms Jinjin Chen (WEHI) will be delivering a workshop on using the standR package from Bioconductor for GeoMX analysis.

What: WS3: Analysis on Nanostring’s GeoMX spatial transcriptomic dataset using Bioconductor package standR
When: Thursday 7th December 2023, 9.30-12:30 pm
Where: Room 230, Andrew N. Liveris Building (46), University of Queensland St Lucia Campus, Brisbane

Prerequisites:

• Bring your own laptop & access to eduroam
• Attendees should have intermediate proficiency in R - there is an assumed level of experience with R as this workshop will not teach R basics.

Who this workshop is for: This workshop is for researchers who have or will work with NanoString GeoMX data as part of their projects.
Learning goals:

• To analyse GeoMx transcriptomics data using standR.
• To perform DE analysis with the GeoMx transcriptomics data using limma.
• To visualize the GSEA results using vissE.

Learning objectives:

• Generate QC plots for the GeoMx transcriptomics data.
• Perform normalisation/batch correction on the GeoMx transcriptomics data.
• Assessing the normalisation/batch correction results.
• Perform differential expression (DE) analysis on the GeoMx transcriptomics data.
• Perform gene set enrichment analysis on the DE results.
• Apply vissE to identify higher-order phenotypes and to visualise the GSEA results.

Developers and team

• Dr Ning Liu, Postdoctoral Fellow, Cancer Systems Biology, SAiGENCI, The University of Adelaide
• Dr Chin Wee Tan, Senior Postdoctoral Fellow, Bioinformatics Division, WEHI
• Ms Jinjin Chen, Postgraduate Student, Bioinformatics Division, WEHI
• Prof Melissa J. Davis, Program Leader, Cancer Systems Biology, SAiGENCI, The University of Adelaide

Registration close 23:59pm, Thursday 6th December.

For more information contact Chin Wee Tan via cwtan@wehi.edu.au