README.md

Teaching Materials for 2024 Spatial Transcriptomics workshop

Prepared by Margaret Ho (NIAID BCBB Science Support)

Day 1: Introduction to spatial transcriptomics methods and concepts for STx data analysis (Nov 4 2024 1-3 pm, online session)

Part 1 - Slides

Day 2: Hands-on workshop using R and Seurat to analyze an example spatial transcriptomics dataset (Nov 15 2024 1-3pm, online session)

Slides For Day 2

Part 2 - Slides

Code For Day 2 to demonstrate Visium (sequencing based) STx data analysis

See Quarto Markdown (Seurat_Visium_Tutorial.qmd) document containing R code for analyzing an example Visium (sequencing-based) STx dataset with Seurat
Part 2 - R Code (Quarto Markdown Document)
Ideally, please run the SETUP section in $${\color{red}red}$$ to install necessary R packages and libraries and download Visium data and scRNA-seq reference dataset before our session starts to make things easier. But no worries if you didn't get to it ahead of time.

PDF (showing the code and output) also available here

Additional Code to demonstrate Xenium (image based) STx data analysis (optional)

See Quarto Markdown document and HTML output in this zip file Seurat_Xenium_tutorial_Biowulf_2024.zip

HPC instructions for Workshop Participants

Running RStudio Server on Biowulf HPC

Biowulf has official instructions for setting up your interactive session, creating a tunnel, and accessing R Studio Server using local host, assigned port and web browser. For additional ease, I created an detailed instructions PDF. I recommend that you request at least 25G of memory for your interactive session for Visium datasets and more (~40GB) for larger datasets such as Visium HD and Xenium.

Running RStudio Server on NIAID Skyline

For running RStudio Server on Skyline, please see Poorani Subramanian's excellent instructions here