SpNeigh
This is the development version of SpNeigh; to use it, please install the devel version of Bioconductor.
Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics
Bioconductor version: Development (3.23)
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.
Author: Jinming Cheng [aut, cre]
Maintainer: Jinming Cheng <jinming.cheng at outlook.com>
citation("SpNeigh")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SpNeigh")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpNeigh")| Getting Started with SpNeigh | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.42 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| 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 |
| System Requirements | |
| URL | https://github.com/jinming-cheng/SpNeigh |
| Bug Reports | https://github.com/jinming-cheng/SpNeigh/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, SeuratObject, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpNeigh_0.99.42.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpNeigh |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpNeigh |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpNeigh/ |
| Package Short Url | https://bioconductor.org/packages/SpNeigh/ |
| Package Downloads Report | Download Stats |