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spatial-transcriptomics-tutorials-with-omicverse

Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering (GraphST, STAGATE), integration, trajectory, communication.

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Starlitnightly
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Starlitnightly
Updated 3/9/2026
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quick start

Installation and usage

Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering (GraphST, STAGATE), integration, trajectory, communication.

Installation
$ install --globalskills.sh
Usage

Once installed, you can use this skill by running the following command in your terminal:

skills use spatial-transcriptomics-tutorials-with-omicverse