SpNeigh
This is the released version of SpNeigh; for the devel version, see SpNeigh.
Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | SpNeigh_1.0.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpNeigh_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | SpNeigh_1.0.0.tgz |
| 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 |