In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Copied from old Giotto, likely needs to be updated for Giotto Suite

Installation

• First time R package installation
• Manual python installation
• Clang error on MacOS
• Error: 'make' not found
• Error converted from warning
• R 3.6.3 and Catalina issue

Data availability

• Where to find seqFISH+ and other ready-to-use datasets?
  Checkout https://github.com/RubD/spatial-datasets to find already preprocessed datasets

• Where to find other spatial datasets?
  Checkout https://www.spatialomics.org/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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.