Tutorials of Spatial Transcriptomics¶

This page mirrors the Space section in mkdocs.yml and provides a markdown entry point for the spatial tutorial notebooks.

Preprocess¶

• Crop and Rotation of spatial transcriptomic data
• Visium 10x HD Cellpose
• Analyze Nanostring data
• Analyze Visium HD data
• Spatial clustering and denoising expressions
• Spatial integration and clustering

Deconvolution¶

• Identifying Pseudo-Spatial Map
• Spatial deconvolution with reference scRNA-seq
• FlashDeconv (fast, GPU-free deconvolution)
• Spatial deconvolution without reference scRNA-seq

Downstream¶

• Spatial transition tensor of single cells
• Spatial Communication
• Spatial IsoDepth Calculation
• Single cell spatial alignment tools