Spatial Transcriptomics

Tutorials for spatial data preprocessing, deconvolution, and downstream analysis.

• Preprocessing
  • Crop and Rotation of spatial transcriptomic data
  • Cell Segmemtation (10x HD)
  • Analyze Nanostring data
  • Analyze Visium HD data
  • Spatial clustering and denoising expressions
  • Spatial integration and clustering
  • Preprocess data
  • Training STAligner model
  • Clustering the space
• Deconvolution
  • Identifying Pseudo-Spatial Map
  • Spatial deconvolution with reference scRNA-seq
  • 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