Package: SVG 1.0.0

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>.

Authors:Zaoqu Liu [aut, cre], SVGbench Contributors [ctb]

SVG_1.0.0.tar.gz
SVG_1.0.0.zip(r-4.7)SVG_1.0.0.zip(r-4.6)SVG_1.0.0.zip(r-4.5)
SVG_1.0.0.tgz(r-4.6-x86_64)SVG_1.0.0.tgz(r-4.6-arm64)SVG_1.0.0.tgz(r-4.5-x86_64)SVG_1.0.0.tgz(r-4.5-arm64)
SVG_1.0.0.tar.gz(r-4.7-arm64)SVG_1.0.0.tar.gz(r-4.7-x86_64)SVG_1.0.0.tar.gz(r-4.6-arm64)SVG_1.0.0.tar.gz(r-4.6-x86_64)
SVG_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SVG/json (API)
NEWS

# Install 'SVG' in R:
install.packages('SVG', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zaoqu-liu/svg/issues

Pkgdown/docs site:https://zaoqu-liu.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

openblascpp

3.70 score 10 scripts 173 downloads 15 exports 3 dependencies

Last updated from:2fb606b28d. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK175
linux-devel-x86_64OK174
source / vignettesOK255
linux-release-arm64OK151
linux-release-x86_64OK148
macos-release-arm64OK85
macos-release-x86_64OK287
macos-oldrel-arm64OK103
macos-oldrel-x86_64OK207
windows-develOK144
windows-releaseOK169
windows-oldrelOK156
wasm-releaseOK139

Exports:ACAT_combinebinarize_expressionbuildSpatialNetworkCalSVGCalSVG_binSpectCalSVG_MarkVarioCalSVG_MERINGUECalSVG_nnSVGCalSVG_SeuratCalSVG_SPARKXgetSpatialNeighbors_DelaunaygetSpatialNeighbors_KNNmoranImoranI_testsimulate_spatial_data

Dependencies:MASSRcppRcppArmadillo

SVG: A Comprehensive R Package for Spatially Variable Gene Detection

Zaoqu Liu

Rendered fromSVG-introduction.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2026-01-23
Started: 2026-01-23