SpNeigh provides methods for neighborhood-aware analysis of spatial transcriptomics data. It supports boundary detection, spatial weighting (centroid- and boundary-based), spatially informed differential expression using spline-based models, and spatial enrichment analysis via the Spatial Enrichment Index (SEI). Designed for compatibility with Seurat objects, SpatialExperiment objects and spatial data frames, SpNeigh enables interpretable, publication-ready analysis of spatial gene expression patterns.

Quick start guide can be found here.

The SpNeigh package can be installed from GitHub by using:

devtools::install_github("jinming-cheng/SpNeigh")

Please cite this article if you use SpNeigh:

Cheng, J.*, Chow, P. K.H., and Liu, N.*. “SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics”. bioRxiv (2025).

(or use BibTex)

@article {Cheng2025SpNeigh,
    author = {Cheng, J. and Chow, P. K.H. and Liu, N.},
    title = {SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics},
    year = {2025},
    doi = {10.1101/2025.11.07.687304},
    journal = {bioRxiv}
}