Frequently Asked Questions#


How do I install an R package for the first time?

Can I install Python components manually?

Data Availability#

Where can I find seqFISH+ and other ready-to-use datasets?

Checkout our GiottoData extension package to find already preprocessed datasets and Giotto mini Objects.

Where else can I find more spatial datasets?

Checkout the following for more spatial -omics data:

How can I automatically download tutorial datasets?

Use getSpatialDataset() from GiottoData:

# Ensure Giotto Suite is installed
if(!"Giotto" %in% installed.packages()) {

# Ensure Giotto Data is installed
if(!"GiottoData" %in% installed.packages()) {

# choose your directory
my_working_dir = getwd()

# merFISH example:

# standard download data to working directory
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir)

# use wget to  download data to working directory (much faster)
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir, method = 'wget')

# avoid certification issues with wget
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir, method = 'wget', extra = '--no-check-certificate')