Package: SpNeigh 1.1.0

Jinming Cheng

SpNeigh: Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

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.

Authors:Jinming Cheng [aut, cre]

SpNeigh_1.1.0.tar.gz
SpNeigh_1.1.0.zip(r-4.7)SpNeigh_1.1.0.zip(r-4.6)SpNeigh_1.1.0.zip(r-4.5)
SpNeigh_1.1.0.tgz(r-4.6-any)SpNeigh_1.1.0.tgz(r-4.5-any)
SpNeigh_1.1.0.tar.gz(r-4.7-any)SpNeigh_1.1.0.tar.gz(r-4.6-any)
SpNeigh_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpNeigh/json (API)

# Install 'SpNeigh' in R:

install.packages('SpNeigh', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jinming-cheng/spneigh/issues

On BioConductor:SpNeigh-1.1.0(bioc 3.24)SpNeigh-1.0.0(bioc 3.23)

spatial singlecell geneexpression differentialexpression transcriptomics software

5.68 score 3 stars 274 downloads 35 exports 180 dependencies

Last updated from:bfc471bc69. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	190
linux-devel-x86_64	OK	357
source / vignettes	OK	265
linux-release-x86_64	OK	314
macos-release-arm64	OK	169
macos-oldrel-arm64	OK	168
windows-devel	OK	262
windows-release	OK	204
windows-oldrel	OK	202
wasm-release	OK	190

Exports:addBoundary addBoundaryPoly boundaryPolyToPoints buildBoundaryPoly colors15_cheng computeBoundaryWeights computeCentroidWeights computeSEI computeSpatialEnrichmentIndex computeSpatialInteractionMatrix extractCoords factorNaturalOrder getBoundary getCellsInside getInnerBoundary getOuterBoundary getRingRegion plotBoundary plotCellsInside plotEdge plotExpression plotInteractionMatrix plotRegion plotSpatialExpression plotStatsBar plotStatsPie plotWeights removeOutliers runLimmaDE runSpatialDE safeColorPalette splineDesign splitBoundaryPolyByAnchor statsCellsInside theme_spneigh

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics bit bit64 bitops blob bslib cachem caTools class classInt cli cluster codetools commonmark concaveman cowplot cpp11 crosstalk curl data.table DBI dbplyr dbscan DelayedArray deldir digest dotCall64 dplyr dqrng e1071 evaluate farver fastDummies fastmap filelock fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle limma listenv lmtest magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises proxy purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rjson rlang rmarkdown ROCR rprojroot RSpectra RSQLite Rtsne s2 S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject sf shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex units utf8 uwot V8 vctrs viridisLite withr wk xfun xtable XVector yaml zoo

Getting Started with SpNeigh

Rendered fromSpNeigh.Rmdusingknitr::rmarkdown

Last update: 2026-04-09
Started: 2025-06-01

Help page	Topics
Add boundary outlines to a spatial ggplot	addBoundary
Add boundary polygons or linestrings to a spatial plot	addBoundaryPoly
Convert boundary polygons to boundary point coordinates	boundaryPolyToPoints
Convert boundary points into valid polygon geometries	buildBoundaryPoly
Custom Color Palette	colors15_cheng
Compute spatial weights based on distance to nearest boundary	computeBoundaryWeights
Compute spatial weights based on distance to the centroid	computeCentroidWeights
Compute Spatial Enrichment Index (SEI)	computeSEI
Compute Spatial Enrichment Index (SEI) for Each Gene	computeSpatialEnrichmentIndex
Compute a spatial neighborhood interaction matrix using K-nearest neighbors (KNN)	computeSpatialInteractionMatrix
Extract spatial coordinates and cluster information	extractCoords
Create a factor with natural (human-friendly) ordering	factorNaturalOrder
Extract spatial boundary points for a cluster or cell population	getBoundary
Identify cells located within spatial boundaries or ring regions	getCellsInside
Generate an inner boundary polygon by shrinking an existing boundary inward	getInnerBoundary
Generate an outer or inner boundary polygon by buffering an existing boundary	getOuterBoundary
Generate ring regions between a boundary and its outer buffer	getRingRegion
Plot spatial cell coordinates with cluster boundaries	plotBoundary
Plot cells located within spatial boundaries or ring regions	plotCellsInside
Plot boundary edges or segmented boundary lines	plotEdge
Plot gene expression across spatial coordinates	plotExpression
Plot a heatmap of a row-scaled spatial interaction matrix	plotInteractionMatrix
Plot filled spatial regions inside boundaries or rings	plotRegion
Plot average gene expression along spatial distance	plotSpatialExpression
Bar plot of cluster statistics for cells inside boundaries or ring regions	plotStatsBar
Pie chart or donut chart of cluster proportions inside spatial regions	plotStatsPie
Plot spatial weights for cells on a spatial plot	plotWeights
Removes spatial outlier cells based on local k-nearest neighbor distances	removeOutliers
Differential expression analysis between two groups of cells using limma	runLimmaDE
Differential expression along spatial distance gradients using splines	runSpatialDE
Generate a safe color palette for discrete clusters	safeColorPalette
Generate an orthonormal spline-based design matrix	splineDesign
Split a polygon boundary into two parts using anchor points	splitBoundaryPolyByAnchor
Summarize cell counts and proportions inside spatial regions	statsCellsInside
Custom ggplot2 theme	theme_spneigh

Package: SpNeigh 1.1.0

SpNeigh: Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)