FAQs#
Frequently Asked Questions#
Installation#
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?
How can I automatically download tutorial datasets?
Use getSpatialDataset() from GiottoData:
# Ensure Giotto Suite is installed if(!"Giotto" %in% installed.packages()) { devtools::install_github("drieslab/Giotto@suite") } library(Giotto) # Ensure Giotto Data is installed if(!"GiottoData" %in% installed.packages()) { devtools::install_github("drieslab/GiottoData") } library(GiottoData) # 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')