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.
Installation
The SpNeigh package can be installed from GitHub by using:
devtools::install_github("jinming-cheng/SpNeigh")Citation
Please cite this article if you use SpNeigh:
To cite SpNeigh in publications, please use:
Cheng J, Chow P, Liu N (2025). "SpNeigh: spatial neighborhood and
differential expression analysis for high-resolution spatial
transcriptomics." _bioRxiv_. doi:10.1101/2025.11.07.687304
<https://doi.org/10.1101/2025.11.07.687304>.
A BibTeX entry for LaTeX users is
@Article{,
title = {SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics},
author = {Jinming Cheng and Pierce Kah Hoe Chow and Nan Liu},
journal = {bioRxiv},
year = {2025},
doi = {10.1101/2025.11.07.687304},
}