'SpaTopic' R package

The 'SpaTopic' R package is centered around the 'SpaTopic' algorithm to infer the spatial tissue architectures from multiplexed images.

Details

The package implements a Collapsed Gibbs sampling algorithm to infer topics, corresponding to distinct tissue microenvironments across multiple tissue images. Without obtaining the cell neighborhood info of every single cell, 'SpaTopic' runs much faster than other KNN-based methods on large-scale images.

The main functions in the 'SpaTopic' package

• Prepare input Seurat5obj_to_SpaTopic

• Model Inference SpaTopic_inference

See also

Useful links:

• https://github.com/xiyupeng/SpaTopic

• Report bugs at https://github.com/xiyupeng/SpaTopic/issues

Author

Xiyu Peng pansypeng124@gmail.com