Package: spatialGE 1.2.2

Oscar Ospina

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

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.

Authors:Oscar Ospina [aut, cre], Alex Soupir [aut], Brooke Fridley [aut], Satija Lab [cph]

spatialGE_1.2.2.tar.gz
spatialGE_1.2.2.tar.gz(r-4.7-arm64)spatialGE_1.2.2.tar.gz(r-4.7-x86_64)spatialGE_1.2.2.tar.gz(r-4.6-arm64)spatialGE_1.2.2.tar.gz(r-4.6-x86_64)
spatialGE_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spatialGE/json (API)

# Install 'spatialGE' in R:

install.packages('spatialGE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

3.42 score 53 scripts 304 downloads 24 exports 226 dependencies

Last updated from:4a24b5f215. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	254
linux-devel-x86_64	OK	299
source / vignettes	OK	328
linux-release-arm64	OK	275
linux-release-x86_64	OK	299
wasm-release	OK	308

Exports:compare_SThet distribution_plots filter_data gene_interpolation get_gene_meta load_images plot_counts plot_image pseudobulk_dim_plot pseudobulk_heatmap pseudobulk_samples spatial_metadata STclust STdiff STdiff_volcano STenrich STgradient SThet STlist STplot STplot_interpolation summarize_STlist tissue_names transform_data

Dependencies:abind annotate AnnotationDbi arrow askpass assertthat assorthead backports base64enc beachmat BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel BiocSingular Biostrings bit bit64 bitops blob boot bslib cachem cellranger checkmate circlize class classInt cli clipr clue cluster codetools colorspace ComplexHeatmap concaveman cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest dir.expiry doParallel dplyr dqrng dynamicTreeCut e1071 EBImage evaluate farver fastmap fftwtools filelock FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomicRanges geometry GetoptLong ggforce ggplot2 ggpolypath ggrepel GlobalOptions globals glue gmp graph gridExtra GSEABase gstat GSVA gtable h5mread HDF5Array hdf5r highr hms htmltools htmlwidgets httr httr2 intervals iotools IRanges irlba isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth khroma knitr labeling lambda.r lattice lifecycle linprog listenv locfit lpSolve magic magick magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mime minqa nlme nloptr numDeriv openssl parallelly pbapply pillar pkgconfig plyr png polyclip prettyunits progress proxy purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppProgress RCurl Rdpack readr readxl reformulas registry rematch reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown ROI RSpectra RSQLite rsvd s2 S4Arrays S4Vectors S7 sass ScaledMatrix scales sctransform Seqinfo sf sfsmisc sftime shape SingleCellExperiment sitmo slam snow sp spacetime spaMM SparseArray sparseMatrixStats sparsesvd SpatialExperiment spData spdep stars stringi stringr SummarizedExperiment sys systemfonts tibble tidyr tidyselect tiff tinytex tweenr tzdb units utf8 uwot V8 vctrs viridisLite vroom withr wk wordspace xfun XML xtable xts XVector yaml zoo

Basic functionality: Visualization, domain detection, and spatial heterogeneity

Installation | Spatially-resolved expression of triple negative breast cancer tumor biopsies | Creating an STList (Spatial Transcriptomics List) | Exploring variation between spatial arrays | Transformation of spatially-resolved transcriptomics data | Visualization of gene expression from spatially-resolved transcriptomics data | Spatial interpolation of gene expression | Unsupervised spatially-informed clustering (STclust) | Association between spatial heterogeneity and sample-level variables | References

Rendered frombasic_functions_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-06-04
Started: 2025-05-13

Help page	Topics
compare_SThet: Compares spatial autocorrelation statistics across samples	compare_SThet
dim: Prints the dimensions of count arrays within an STList object.	dim,STlist-method
per_unit_counts: Generates distribution plots of spot/cell meta data or gene expression	distribution_plots
filter_data: Filters cells/spots, genes, or samples	filter_data
gene_interpolation: Spatial interpolation of gene expression	gene_interpolation
get_gene_meta: Extract gene-level metadata and statistics	get_gene_meta
load_images: Place tissue images within STlist	load_images
plot_counts: Generates plots for the distribution of counts	plot_counts
plot_image: Generate a ggplot object of the tissue image	plot_image
pseudobulk_dim_plot: Plot PCA of pseudobulk samples	pseudobulk_dim_plot
pseudobulk_heatmap: Heatmap of pseudobulk samples	pseudobulk_heatmap
pseudobulk_samples: Aggregates counts into "pseudo bulk" samples	pseudobulk_samples
show: Prints overview of STList oject.	show,STlist-method
spatial_metadata: Prints the names of the available spot/cell annotations	spatial_metadata
STclust: Detect clusters of spots/cells	STclust
STdiff: Differential gene expression analysis for spatial transcriptomics data	STdiff
STdiff_volcano: Generates volcano plots from STdiff results	STdiff_volcano
STenrich	STenrich
STgradient: Tests of gene expression spatial gradients	STgradient
SThet: Computes global spatial autocorrelation statistics on gene expression	SThet
STlist: Creation of STlist objects for spatial transcriptomics analysis	STlist
Definition of an STlist object class.	STlist-class
STplot: Plots of gene expression, cluster memberships, and metadata in spatial context	STplot
STplot_interpolation: Visualize gene expression surfaces	STplot_interpolation
summarize_STlist: Generates a data frame with summary statistics	summarize_STlist
summary: Prints overview of STList oject.	summary,STlist-method
tissue_names: Prints the names of the tissue samples in the STlist	tissue_names
transform_data: Transformation of spatial transcriptomics data	transform_data

Package: spatialGE 1.2.2

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

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