wSIR: Weighted Sliced Inverse Regression for supervised dimension reduction of spatial transcriptomics and single cell gene expression data
This is an R package for computation of the wSIR low-dimensional embedding of gene expression data, using its spatial coordinates. It includes functions to analyse the resulting low-dimensional space, as well as the mapping from high-dimensional gene expression data to low-dimensional space. There is a function to project new gene expression data (where the spatial coordinates are unknown) into a low-dimensional space which has the ability to predict each cell’s spatial location.
For an overview of the method and examples, see the vignette at this website.