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Raw object(Seurat v5): obj_raw.rds
This RDS object is an unprocessed Seurat object containing raw spatial single-cell RNA sequencing data. It has not undergone any normalization, scaling, or filtering.
Annotated object(Seurat v5): obj_final.rds
This RDS object has been processed using SCTransform and includes cell type annotations from three methods: marker-based, reference-based, and anchor-based. It also contains results from several analyses:
- 1. Differential Expression Analysis (DEG):
- • Stored in obj@misc$DEG
- 2. Spatial Colocalization Analysis (hoodscanR):
- • Results in obj@misc$spe
- 3. Spatial Cellular Communication Analysis (Cellchat):
- • Stored in obj@misc$cellchat
- 4. Niche Analysis:
- • Proportions in obj@misc$niche
- • ssGSEA pathway analysis in obj@misc$heatmap