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# SpNeigh <img src="man/figures/SpNeigh_logo.png" align="right" alt="" width="120" />

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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},
      }
