Initial formatting of Slide-Seq data to work with Seurat and Kandinsky
prepare_slideseq_seurat(path = NULL, dataset.id = NULL, pattern = NULL)character string specifying the path to the Slide-Seq input files directory
character string that will be used to name the output Seurat object identity
character string that will be used as a key to identify Slide-Seq input file names in case when input files from multiple Slide-Seq samples/slides are stored in the same directory
a Seurat object containing Slide-Seq count matrix, metadata, and spatial coordinates to be used for downstream analysis with Kandinsky functions
This function will use Slide-Seq input data to build a new Seurat object. All Slide-Seq input files must be stored in the same folder that will be specified to call the function. Kandinsky expects to find Slide-Seq files in the same format proposed in the Slide-Seq V2 original study https://singlecell.broadinstitute.org/single_cell/study/SCP815/sensitive-spatial-genome-wide-expression-profiling-at-cellular-resolution#study-summary
Other prepare_data:
prepare_cosmx_seurat(),
prepare_g4x_seurat(),
prepare_merscope_seurat(),
prepare_proseg_seurat(),
prepare_visiumHD_seurat(),
prepare_visium_seurat(),
prepare_xenium_seurat()