1 Getting started

1.1 Summary

This workshop will cover Spatial Tanscriptomics Analysis

Conducted by : |Dr. Shani Amarasinghe (Jardè lab, Monash BDI & Monash Genomics and Bioinformatics Platform) |Dr. Adrew Pattinson (Jardè lab,) |Dr. Sean Byars (Monash Genomics and Bioinformatics Platform)

In short: Spatial transcriptomics helps connect molecular function with physical structure, enabling a deeper understanding of biological systems. These insights are not easily captured by bulk or single-cell RNA-seq alone. Spatial methods provide the missing layer: where things are happening.

Goal: Equip you with the foundational knowledge and hands-on skills to start working with spatial transcriptomics data across multiple platforms.

1.2 Prerequisies and dependencies

programs, R and Python packages

Data sources: Xenium Data

packages

install.packages(“qs”)