Spatial Transcriptomics# Tutorials for spatial data preprocessing, clustering, deconvolution, and downstream analysis. Preprocessing Crop and Rotation of spatial transcriptomic data Cell Segmentation (10x HD) Analyze NanoString data Analyze Xenium data Analyze 10x Atera (WTA Preview) FFPE breast cancer data Analyze Visium HD data Spatial integration and clustering Preprocess data Training STAligner model Clustering the space Clustering Spatial clustering with GraphST + pymclustR Spatial clustering with BINARY + pymclustR Spatial clustering with STAGATE + pymclustR Spatial clustering with CAST + pymclustR Spatial clustering with BANKSY + pymclustR Deconvolution Identifying Pseudo-Spatial Map Spatial deconvolution with reference scRNA-seq Spatial deconvolution with RCTD FlashDeconv: Fast Spatial Deconvolution via Structure-Preserving Sketching Spatial deconvolution without reference scRNA-seq Downstream Spatial transition tensor of single cells Spatial Communication Spatial IsoDepth Calculation Single cell spatial alignment tools
