Past Workshops
10x Genomics Spatial Workshop Series – Three Sessions
Because cells reside within microenvironments, their functions are influenced by the network cells surrounding them, sending and receiving messages. Spatially resolved biology, including whole transcriptomic and targeted in situ methods, allows scientists to build a more complete view of cellular function in a morphological context, representing a paradigm shift in the study of biological systems. Visium from 10x Genomics is a NGS-based spatial discovery platform that allows whole transcriptome profiling of tissues. The Xenium In Situ platform is an imaging-based solution that provides precise localization of thousands of RNA targets with subcellular resolution, offering true single cell spatial analysis. Insights from these spatial techniques can be combined with single cell data to bring greater resolution and enable a deeper understanding of gene expression patterns, helping researchers develop and refine hypotheses.
January 11, 2024 – Visium
January 18, 2024 – Xenium
January 24, 2024 – Visium Gene Expression
Spatial Transcriptomic Data Analysis & Software
Genomics Research and Technology Hub (GRT Hub) Workshop
Required: Personal laptop (Mac or Windows) and HPC3 account
Instructors: Jenny Wu, PhD and Ivan Chang, PhD
This workshop introduces data analysis workflow with both sequencing and imaging based spatial transcriptomics platforms, using 10x Visium and Xenium as examples. The topics included an overview of data quality control, preprocessing and visualization, cellular segmentation etc. with 10x proprietary software and state of the art Open-source software. A guided tour was 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.
- Computing on the HPC3 for Spatial Omics Ivan Chang, PhD
- Introduction to 10x 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
- Introduction to 10x Visium and Xenium Spatial Platform Data Analysis, Jenny Wu, PhD
Bioinformatics & Computational Biology | R Programming
The Genomics Research and Technology Hub conducted a workshop on Computational Biology and R Programing. The GRT Hub is working with Eduard Mas, PhD, in the Fleischman laboratory, to bring you an introductory course in R. It will take you from start up to packages including graphical displays and beyond to package development. (This is a repeat of the course that was offered and very popular this fall.)
Session Recordings
November 28
November 30
December 5
December 7
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