This package will automatically download the spatial locations and expression matrix for the chosen dataset. These files are already in the right format to create a Giotto object. If wget is installed on your machine, you can add 'method = wget' to the parameters to download files faster.
getSpatialDataset( dataset = c("ST_OB1", "ST_OB2", "codex_spleen", "cycif_PDAC", "starmap_3D_cortex", "osmfish_SS_cortex", "merfish_preoptic", "seqfish_SS_cortex", "seqfish_OB", "slideseq_cerebellum"), directory = getwd(), ... )
| dataset | dataset to download |
|---|---|
| directory | directory to save the data to |
| ... | additional parameters to |