Discovery of cell-type specific gene programs from spatial transcriptomics data. This workflow starts from an annotated xenium dataset.
1. Correcting transcript diffusion with scvi-tool (ResolVI)
2. Extract patient-level cell-type of interest
3. Run cNMF on individual samples
4. Merge programs
5. Convert to h5 file
6. Move to R.studio for Metaprogram clustering