R Observatory: Metrics for SVG version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SVG

1.0.0

Spatially Variable Genes Detection Methods for Spatial Transcriptomics

0packages depend

1.4Kdownloads / year

46.2%test coverage

13/13checks pass

Overview

About

Maintained by Zaoqu LiuFirst published 2026-02-011 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SVG", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Zaoqu-Liu/SVG")

Development version from Zaoqu-Liu/SVG. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-svg

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SVG

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SVG

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.15

46.2%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 577 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 100%
References docs: 27%

Downloads

1.4K

CRAN downloads in the past year

Rank #18,601 · ~4/day · ~119/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

59090 days

1.4K1 year

Compare downloads with other packages →

Also on238 r2u23 autocran

Repository

GitHub ↗ zaoqu-liu/svg

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-01-23

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/zaoqu-liu/svg on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

parallelstatsutilsmethodsMASSRcpp

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (14)

BRISC geometry RANN CompQuadForm BiocParallel SpatialExperiment SingleCellExperiment SummarizedExperiment spatstat.geom spatstat.explore testthat knitr rmarkdown covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Zaoqu Liu

Author, Maintainer

Authors (1)

Zaoqu Liu

Author, Maintainer

Contributors (1)

SVGbench Contributors

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-01
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 198 KB / 1 file
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SVG")

Format

Liu, Z., & Contributors, S. (2026). SVG: Spatially Variable Genes Detection Methods for Spatial Transcriptomics (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SVG

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SVG version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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