Profile:
Professor Melissa Davis is the program leader of Computational Systems Oncology at the South Australian Immunogenomics Cancer Institute, based at the University of Adelaide. Professor Davis also has honorary appointments at The University of Melbourne, The University of Queensland and The Walter and Eliza Hall Institute of Medical Research, and her multi-disciplinary research team is based across both Melbourne and Adelaide. Professor Davis is an internationally recognised expert in computational systems oncology, with work both at the methodological and the biological ends of the computational biology spectrum. Her team is committed to the development of high quality software implementing their methods, making these techniques available to the international research community through web-based applications, software packages, published protocols, data packages, and practical workshops.
Talk title:
Methods for multi-scale analysis of spatial transcriptomics data
Spatial molecular measurement technologies not only generate measurements of abundance, they provide spatial information about the distribution of these molecules. Features in spatial data emerge across many scales of resolution, from clusters within cells to shapes that highlight tissue architecture. I will describe three different methods for analysis of data covering both GeoMx and CosMx platforms: (i) StandR is a structured data analysis pipeline for GeoMx transcriptomic data that includes quality assessment, batch correction and normalisation, and supports the analysis of the complex experimental designs typical in spatial experiments; (ii) HoodScanR is our newest package that performs neighborhood analysis at the individual gene, pathway or cell type level and (iii) vissE is a web-based tool that performs functional analysis of whole spatial experiments, identifying regions of pathway activity and providing a data-driven method for the identification and clustering of gene expression signatures with variable patterns in spatial data.