Initial formatting of Xenium data to work with Seurat and Kandinsky
prepare_xenium_seurat(path = NULL, dataset.id = "X", h5 = TRUE)character string specifying the path to the Xenium input files directory
character string that will be used to name the output Seurat object identity
boolean, whether reading count matrix from 'cell_feature_matrix.h5' (TRUE) file or zipped 'cell_feature_matrix.tar.gz' folder (FALSE)
a Seurat object containing Xenium count matrix, metadata, and additional files/file paths to be used for downstream analysis with Kandinsky functions
This function will use 10X Xenium raw input data to build a new Seurat object. All Xenium input files must be stored in the same folder that will be specified to call the function
Other prepare_data:
prepare_cosmx_seurat(),
prepare_g4x_seurat(),
prepare_merscope_seurat(),
prepare_proseg_seurat(),
prepare_slideseq_seurat(),
prepare_visiumHD_seurat(),
prepare_visium_seurat()