Package: SpNeigh
Title: Spatial Neighborhood Modeling and Differential Expression
        Analysis for Transcriptomics
Version: 1.1.0
Authors@R: 
    person(given = "Jinming", 
           family = "Cheng", 
           email="jinming.cheng@outlook.com", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-3806-4694"))
Description: 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.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
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)
biocViews: Spatial, SingleCell, GeneExpression, DifferentialExpression,
        Transcriptomics, Software
URL: https://github.com/jinming-cheng/SpNeigh
BugReports: https://github.com/jinming-cheng/SpNeigh/issues
Depends: R (>= 4.4.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        libglpk-dev make libmagick++-dev gsfonts libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libproj-dev python3
        libsqlite3-dev libudunits2-dev libnode-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:43 UTC
RemoteUrl: https://github.com/bioc/SpNeigh
RemoteRef: HEAD
RemoteSha: bfc471bc69896c75d10c3f21f38fd6cf4c049066
NeedsCompilation: no
Packaged: 2026-05-30 09:47:36 UTC; root
Author: Jinming Cheng [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3806-4694>)
Maintainer: Jinming Cheng <jinming.cheng@outlook.com>
Built: R 4.6.0; ; 2026-05-30 10:22:58 UTC; windows
