NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data. In particular, given an index and a niche cell type, we define an (index,niche) niche gene as a gene as a gene that is up or down-regulated in the index cell type when in the presence of the niche cell type.
NicheDE identifies (index,niche)+ genes by first characterizing a cell’s neighborhood into a vector called the effective niche. Then, by regressing gene expression on the effective niche,testing if certain coefficients are equal to 0 is equivalent to determining if the gene is an (index,niche) niche gene.
For more information about this method please check out the manuscript

Installation

You can install NicheDE with the following code

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
install.packages("devtools")
options(timeout=9999999)
devtools::install_github("kaishumason/NicheDE") # install
library(nicheDE)

Vignette

Click the link below for a tutorial on using nicheDE
NicheDE Tutorial: All Steps

Citation

Kaishu Mason, Anuja Sathe, Paul Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Hanlee P. Ji, Nancy Zhang Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions (Biorxiv 2023: https://doi.org/10.1101/2023.01.03.522646)