Datasets

The datasets are all from publicly available datasets. Specifically,

  1. The spatial data of human dorsolateral prefrontal cortex(DLPFC), which was generated from the 10x Genomics Visium platform can be accessed in the spatialLIBD package. The reference scRNA-seq data of DLPFC, which has 78,886 nuclei from 34 brain samples was generated in a previous study and you can download it from GEO using the accession number: GSE144136.

  2. Two spatial data of mouse posterior brain and anterior brain generated by 10x Genomics were downloaded from anterior and posterior. The reference scRNA-seq data with 28706 cells in 29 classes is downloaded with the accession number: GSE115746. After removing obscure classes such as “’Batch Grouping”, there are 23 classes are left. You can download it here.

  3. Human spatial transcriptomic data of SCC is available at GEO accession GSE144240. The corresponding human SCC scRNA-seq reference data available at GEO accession GSE144236.