R Observatory: Metrics for spatialGE version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spatialGE

1.2.2

Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

0packages depend

3.1Kdownloads / year

–test coverage

9/13checks pass

Overview

About

Maintained by Oscar OspinaFirst published 2025-05-133 releasesCRAN page ↗

Visualization and analysis of spatially resolved transcriptomics data. The 'spatialGE' R package provides methods for visualizing and analyzing spatially resolved transcriptomics data, such as 10X Visium, CosMx, or csv/tsv gene expression matrices. It includes tools for spatial interpolation, autocorrelation analysis, tissue domain detection, gene set enrichment, and differential expression analysis using spatial mixed models.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-spatialge

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

Health

CRAN checks

4ERROR9OK

Failing flavors

ERROR r-devel-linux-x86_64-debian-clang
ERROR r-devel-linux-x86_64-debian-gcc
ERROR r-release-linux-x86_64
ERROR r-release-macos-x86_64

Slowest check: 5.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

45

Dependencies · direct

Check history

ERROR2026-04-09
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
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 · 352 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.1K

CRAN downloads in the past year

Rank #14,123 · ~9/day · ~262/mo

Releases R versions

Daily download trend is not available in this view yet.

24530 days

72590 days

3.1K1 year

Compare downloads with other packages →

Also on390 r2u

Dependencies

Declared dependencies

58 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (45)

arrow BiocParallel concaveman ComplexHeatmap data.table DelayedArray DelayedMatrixStats dynamicTreeCut dplyr EBImage ggforce ggplot2 ggpolypath ggrepel gstat GSVA hdf5r jpeg jsonlite khroma magrittrMatrixMASSmethodsparallelpng RColorBrewer Rcpp readr readxl rlang scales sctransform sfsmisc sf sp spaMM spdepstatsstringr tibble tidyrutilsuwot wordspace

LinkingTo (3)

Rcpp RcppEigen RcppProgress

Suggests (17)

curl geoR ggpubr httr janitor kableExtra knitr msigdbr progress rmarkdownrpartR.utils scSpatialSIM spatstat SeuratObject tidyverse testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Oscar Ospina

Author, Maintainer

Authors (3)

Oscar Ospina

Author, Maintainer

Brooke Fridley

Author

Alex Soupir

Author

Copyright holders (1)

Satija Lab

Copyright holder

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.2Latest
2025-06-04 · current release · diff ↗
unarchivedReturned to CRAN
2025-06-04
archivedRemoved from CRAN
2025-05-27
repeated policy violation On Internet access, even on resubmission
1.2.1
2025-05-26 · diff ↗
1.2.0
2025-05-13
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-13
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
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("spatialGE")

Format

Ospina, O., Satija Lab, Fridley, B., & Soupir, A. (2025). spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression (Version 1.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.spatialGE

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 spatialGE version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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