The package SPATAData gives access to our data base of spatial transcriptomic samples. Furthermore, it provides easy access to data sets that have been already published. We are continuously updating this collection so make sure to check for package updates on a regular basis. Please not that several of these data sets are not owned by us! Make sure to use the correct citation if you download and use them for your analysis. See more under Citation.
Install with:
library(devtools)
# if you have not already
devtools::install_github("kueckelj/confuns")
# installs the package
devtools::install_github("theMILOlab/SPATAData")
Downloaded SPATA2 objects can be used within the SPATA2 package. More info: https://themilolab.github.io/SPATA2/
If you used SPATA2 or SPATAData for your analysis pease consider citing:
Kueckelhaus, J., Frerich, S., Kada-Benotmane, J. et al. Inferring histology-associated gene expression gradients in spatial transcriptomic studies. Nat Commun 15, 7280 (2024). https://doi.org/10.1038/s41467-024-50904-x