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SVG: Spatially Variable Genes Detection Methods for Spatial Transcriptomics

A unified framework for detecting spatially variable genes (SVGs) in spatial transcriptomics data. This package integrates multiple state-of-the-art SVG detection methods including 'MERINGUE' (Moran's I based spatial autocorrelation), 'Giotto' binSpect (binary spatial enrichment test), 'SPARK-X' (non-parametric kernel-based test), and 'nnSVG' (nearest-neighbor Gaussian processes). Each method is implemented with optimized performance through vectorization, parallelization, and 'C++' acceleration where applicable. Methods are described in Miller et al. (2021) <doi:10.1101/gr.271288.120>, Dries et al. (2021) <doi:10.1186/s13059-021-02286-2>, Zhu et al. (2021) <doi:10.1186/s13059-021-02404-0>, and Weber et al. (2023) <doi:10.1038/s41467-023-39748-z>.

Version: 1.0.0
Depends: R (≥ 4.0.0)
Imports: parallel, stats, utils, methods, MASS, Rcpp (≥ 1.0.0)
LinkingTo: Rcpp, RcppArmadillo
Suggests: BRISC, geometry, RANN, CompQuadForm, BiocParallel, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, testthat (≥ 3.0.0), knitr, rmarkdown, covr
Published: 2026-02-01
DOI: 10.32614/CRAN.package.SVG (may not be active yet)
Author: Zaoqu Liu ORCID iD [aut, cre], SVGbench Contributors [ctb] (Original method implementations)
Maintainer: Zaoqu Liu <liuzaoqu at 163.com>
BugReports: https://github.com/Zaoqu-Liu/SVG/issues
License: MIT + file LICENSE
URL: https://github.com/Zaoqu-Liu/SVG, https://zaoqu-liu.github.io/SVG/
NeedsCompilation: yes
Materials: README, NEWS
CRAN checks: SVG results

Documentation:

Reference manual: SVG.html , SVG.pdf
Vignettes: SVG: A Comprehensive R Package for Spatially Variable Gene Detection (source, R code)

Downloads:

Package source: SVG_1.0.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: SVG_1.0.0.zip
macOS binaries: r-release (arm64): SVG_1.0.0.tgz, r-oldrel (arm64): SVG_1.0.0.tgz, r-release (x86_64): SVG_1.0.0.tgz, r-oldrel (x86_64): SVG_1.0.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SVG to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.