SpNeigh
Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics
Bioconductor version: 3.24 · Package version: 1.1.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpNeigh")Details
| Maintainer | Jinming Cheng <jinming.cheng@outlook.com> |
| Author | Jinming Cheng [aut, cre] (ORCID: <https://orcid.org/0000-0003-3806-4694>) |
| License | GPL (>= 3) |
| URL | https://github.com/jinming-cheng/SpNeigh |
| Bug Reports | https://github.com/jinming-cheng/SpNeigh/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/SpNeigh/ |
Citation
From within R, enter citation("SpNeigh"):
Jinming Cheng. SpNeigh: Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics. doi:10.18129/B9.bioc.SpNeigh, R package version 1.1.2, https://bioconductor.org/packages/SpNeigh.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpNeigh_1.1.2.tar.gz |
| Windows binary (x86_64) | SpNeigh_1.1.2.zip |
| macOS binary (arm64) | SpNeigh_1.1.2.tgz |
| macOS binary (x86_64) | SpNeigh_1.1.2.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: concaveman, dbscan, dplyr, FNN, ggplot2, limma, magrittr, Matrix, methods, patchwork, purrr, rlang, scales, Seurat, sf, SingleCellExperiment, SpatialExperiment, splines, stringr, SummarizedExperiment, tibble, tidyr
Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, testthat (>= 3.0.0)