getSpatialDataset: getSpatialDataset

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

getSpatialDataset

Description

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.

Usage

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

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.