Last updated: 2024-11-02
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Knit directory: spatialsnippets/
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These examples are a sampler of tests that can be performed on an in-situ single cell spatial datasets. Initial examples use cosMX, though approaches should be valid on other platforms like Xenium.
Further details on the papers, tools, statistics and methods are linked from each page.
Each example presents just one way of doing things (and currently only with Seurat) - there are many, many other approaches! These are intended as a starting point.
Single cell spatial
Single cell RNAseq
These examples assume that the data has been loaded, preprocessed (e.g. QC-ed, UMAP) and annotated (e.g. sample names, cell types, cell niches). For information on how each dataset was prepared, see the data tab.