FAQs#

Frequently Asked Questions#

Installation#

First time R package installation

Manual python installation

Errors on MacOS

Errors on Windows

Error converted from warning

Data Availability#

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

Checkout RubD/spatial-datasets to find already preprocessed datasets

Where to find other spatial datasets?

Checkout SpatialDB to download expression matrix and location information

How to automatically download tutorial datasets? (merFISH example)
# choose your directory
my_working_dir = getwd()

# 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')

# see download.file for more options
?download.file