CSHL Single Cell Biology Core
Spatial Biology Club
June 2024
Speakers:
Jon Preall
Spatial 'Omics at the Single Cell Core
Claire Regan
Getting Started with Visium
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
stLearn (requires python 3.8 which can make it a bit challenging to include in an environment)
Next
Meeting:
July 29th
Upcoming Meetings:
August 26th
July 2024
Speakers:
Jon Preall
Xenium at the Single Cell Core
Anita Ng
Exploring CLL with CellDive and Halo
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
stLearn (requires python 3.8 which can make it a bit challenging to include in an environment)
Other tools:
August 2024
Bring Your Own Data Workshop
September 2024
Speakers:
Claire Regan
Visium HD ABCs: Artifacts, Binning and Cell Typing
Andrew Shih
Annotating Tissue Architecture with HALO AI
General Resources and Tutorials:
Awesome Spatial Omics Github and Awesome Single Cell Github
Guidebook of Spatial Transcriptomics Review
Best Practices for Spatial Transcriptomics Analysis with Bioconductor
Some packages to check out:
R Packages:
Python Packages:
October 2024
Andrew Ji
Probing the single-cell spatial transcriptomic landscape of human skin across anatomic sites
December 2024
Li Yuan
High-Throughput Neural Projection Mapping with Axonal BARseq: Exploring Methodology and Analysis
June 2025
Jon Preall
How to Run 40-plex IF at the Core with Lunaphore COMET
