The spaVAE model for spatially resolved transcriptomics (SRT).
The spaLDVAE (spaVAE with linear decoder) and spaPeakLDVAE models for detecting spatial variable genes and peaks.
The spaVAE model for integrating batches of SRT data.
The spaPeakVAE model for spatial ATAC-seq data.
The spaMultiVAE model for spatial multiomics data (transcriptomics and surface protein).
Source code of some utilities, including louvaining clustering, clustering refinement, and calculating Moran's I.