SpatiaBio Tutorials

Code and notebooks from spatiabio.com — a blog covering spatial transcriptomics and single-cell genomics. Every analysis here is run on real data with verified outputs.

Posts & Notebooks

#	Post	Notebook
1	Squidpy vs Seurat: A Practical Comparison	squidpy-vs-seurat/squidpy_vs_seurat.ipynb
2	Squidpy + Seurat Troubleshooting Roundup	troubleshooting/squidpy_seurat_troubleshooting.ipynb
3	Spatio-DARLIN: The Paper That Maps Where Cells Have Been	spatio-darlin/spatio_darlin_explainer.ipynb
4	CellChat on Spatial Data: A Step-by-Step Tutorial	cellchat-spatial/cellchat_spatial_tutorial.ipynb
5	Spatially Variable Genes with Squidpy: Moran's I	svg-morans-i/svg_morans_i.ipynb
6	Visualizing Spatially Variable Genes with Squidpy	svg-visualization/svg_visualization.ipynb
7	Neighborhood Enrichment Analysis with Squidpy	nhood-enrichment/nhood_enrichment.ipynb
8	Co-occurrence Analysis with Squidpy	co-occurrence/co_occurrence.ipynb
9	Ligand-Receptor Interactions with Squidpy	ligrec/ligrec.ipynb
10	Complete Squidpy Spatial Transcriptomics Workflow	complete-workflow/complete_workflow.ipynb

Data

Tutorials use publicly available datasets:

• visium_hne_adata — 10x Genomics Visium mouse brain (built into squidpy)
• stxBrain — 10x Genomics Visium mouse brain anterior (SeuratData)
• sc_mouse_cortex — Allen Brain Atlas scRNA-seq mouse cortex

Environment

pip install squidpy scanpy

R tutorials require: Seurat, SeuratData, CellChat

About

Posts are written by Lociven. All code is executed before publication.
Full writeups at spatiabio.com.