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Spatial Biology Club

The next meeting of Spatial Biology Club is on: July 30th, 2024 4 pm

Past Meetings:

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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

Segmentation of Visium HD

Example Datasets

Some packages to check out:

R Packages:

Seurat

Giotto

BayesSpace

STdeconvolve 

SpatialExperiment

Python Packages:

Scanpy

Squidpy

stLearn (requires python 3.8 which can make it a bit challenging to include in an environment) 

Cell2Location 

SpatialData 

StarDist

cellpose

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