Workshops

This workshop will introduce data analysis workflow with both sequencing and imaging based spatial transcriptomics platforms, using 10x Visium HD and Xenium as examples. The topics will include an overview of preprocessing and data visualization with both 10x proprietary software and the state-of-the-art open-source software. New topics will be discussed including analysis, spatial neighborhood analysis and integration with image data. A guided tour will be provided on how to run the latest visualization and data exploration tools to support spatial transcriptomics via both the command line and the Jupyterhub of HPC3. Attendees are encouraged to bring their own project data for analysis and discussion.

Introduction to 10x Genomics Visium and Xenium Spatial Platform Data Analysis Workflow and Analytical Tools (Jenny Wu, PhD)

Interactive Computing on the HPC3 for Spatial Omics (Ivan Chang, PhD)