<!-- README.md is generated from README.Rmd. Please edit that file --> # SpNeigh <img src="man/figures/SpNeigh_logo.png" align="right" alt="" width="120" /> <!-- badges: start --> [](https://github.com/jinming-cheng/SpNeigh/actions) [](https://app.codecov.io/gh/jinming-cheng/SpNeigh) <!-- badges: end --> 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](https://jinming-cheng.github.io/SpNeigh/articles/SpNeigh.html). ## Installation Install *SpNeigh* from Bioconductor ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("SpNeigh") ``` Or install *SpNeigh* from GitHub: ``` r 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 (2026). "SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics." _NAR Genomics and Bioinformatics_, *8*, lqag039. doi:10.1093/nargab/lqag039 <https://doi.org/10.1093/nargab/lqag039>. 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 = {NAR Genomics and Bioinformatics}, year = {2026}, volume = {8}, pages = {lqag039}, doi = {10.1093/nargab/lqag039}, }