getSpatialDataset

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", "ST_SCC"),
  directory = getwd(),
  verbose = TRUE,
  ...
)

Arguments

dataset

dataset to download

directory

directory to save the data to

verbose

be verbose

...

additional parameters to download.file