R Observatory: Metrics for spatialGE version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spatialGE

1.2.2Package record

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

0packages depend

3.3Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Oscar OspinaCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-patched-linux-x86_64

Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 4.8 min · r-devel-windows-x86_64

Status changes

ERROR12 OK, 1 ERROR2026-10-15
OK13 OK2026-10-08
ERROR12 OK, 2 ERROR2026-04-09
OK14 OK2026-03-16
ERROR13 OK, 1 ERROR2026-03-13

Show 1 earlier changeHide 1 earlier change

OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMEYes · 352 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 28
Examples that run: 0%14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 58%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

spatialge_tutorial_main HTML

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #10,081 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

39930 days

1K90 days

3.3K1 year

Compare downloads with other packages →

Also on360 r2u

How downloads are counted

Dependencies

Declared dependencies

58 external dependencies (excludes base and recommended)

Installing spatialGE adds 126 packages (78 with compiled code, 122 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, sf 9.3 MB. 6 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (4)

Oscar Ospina

Author, Maintainer since 1.2.0 (2025)

Brooke Fridley

Author

Alex Soupir

Author

Satija Lab

Copyright holder

Copyright holder of code fragments from Seurat function FindVariableFeatures

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-06-04
1.2.2Latest
record
2025-06-04 · current release · diff ↗
archivedRemoved from CRAN
2025-05-27
repeated policy violation On Internet access, even on resubmission
1.2.1
record
2025-05-26 · diff ↗
1.2.0
record
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
Copyright: ins/COPYRIGHT
Download size: 1.1 MB

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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