The Visium HD Spatial Gene Expression Data Analysis Workshop

In this hands-on workshop, you'll embark on the Visium HD Spatial Gene Expression data analysis journey with us. Using human colon cancer sample data, we’ll begin by processing raw data with Space Ranger on the 10x Cloud Analysis platform. Next, we'll assess data quality using the web summary and dive into Loupe Browser for manual image alignment, in-depth data exploration, and cell-type mapping. We’ll then take these insights to community-developed tools, further exploring the tumor microenvironment through pathway analysis. To conclude, each participant will have the opportunity to discuss their own analysis roadmap with guidance from 10x Genomics experts.

Primary goal

Demystify the data analysis process for customers with a hands-on, active learning approach for Visium HD

Target audience

People who have or will soon have Visium HD data and have limited to no bioinformatics experience with Visium HD

Program

• Introduction

• 10x Cloud Analysis: from FASTQs to quantitative biological information with Space Ranger for Visium HD

• Overview of Visium HD spatial data analysis

• Quality assessment: interpreting the Space Ranger web summary

• Loupe Browser: manual image alignment, data exploration and cell-type mapping

• Introducing community-developed tools for Visium data analysis

• Further analysis using community tools: GSEA as an example

• Wrap up and optional chat with the 10x team