An R/Bioconductor software tool to identify genes associated with latent space interactions in spatial transcriptomics.
This tutorial aims to help user to apply SpaceMarkers on spatial Quantitative Pharmacology (spQSP) model.
If you use the SpaceMarkers software please cite:
Atul Deshpande, Melanie Loth, et al., Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces. bioRxiv 2022. doi:10.1101/2022.06.02.490672
You can install SpaceMarkers directly from the Github source.
install.packages("remotes")
remotes::install_github("FertigLab/SpaceMarkers", dependencies = TRUE, build_vignettes = TRUE)
The sample result for running the code is stored in /sample_result folder
$ R_SCRIPT = "spQSP_SplnMarkers.R' 'sample_result'
$ Rscript $R_SCRIPT