nnSVG
This is the development version of nnSVG; for the stable release version, see nnSVG.
All Bioconductor versions of nnSVG
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Bioconductor version: 3.24 · Package version: 1.17.1
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.
Author: Lukas M. Weber [aut, cre] 
, Stephanie C. Hicks [aut]
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
Citation
From within R, enter citation("nnSVG"):
Lukas M. Weber, Stephanie C. Hicks. nnSVG: Scalable identification of spatially variable genes in spatially-resolved transcriptomics data. doi:10.18129/B9.bioc.nnSVG, R package version 1.17.1, https://bioconductor.org/packages/nnSVG.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("nnSVG")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.17.1 |
| License | MIT + file LICENSE |
| URL | https://github.com/lmweber/nnSVG |
| Bug Reports | https://github.com/lmweber/nnSVG/issues |
| Last updated | 2026-07-14 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4 years) |
| Downloads rank | 992 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/nnSVG/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("nnSVG")| nnSVG Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | nnSVG_1.17.1.tar.gz |
| Windows binary (x86_64) | nnSVG_1.17.1.zip |
| macOS binary (arm64) | nnSVG_1.17.1.tgz |
| macOS binary (x86_64) | nnSVG_1.17.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nnSVG |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nnSVG |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.2)
Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods
Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat