Workshops

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

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.)

Workshop Agenda

Session Recordings

November 28

• Intro to R
• Intro to R (cont.) and Data Management

November 30

• Data Management (Part 1)
• Data Management (Part 2)

December 5

• Basic Plots
• Functions and Basic Programming

December 7

• Efficient R Programming & Object-Orientated Programming
• Advanced Data Visualization & R Packages