spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression (original) (raw)
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.
Version:
1.2.2
Imports:
arrow, BiocParallel, concaveman, ComplexHeatmap, data.table, DelayedArray, DelayedMatrixStats, dynamicTreeCut, dplyr, EBImage, ggforce, ggplot2, ggpolypath, ggrepel, gstat, GSVA, hdf5r, jpeg, jsonlite, khroma (≥ 1.6.0), magrittr, Matrix, MASS, methods, parallel, png, RColorBrewer, Rcpp (≥ 1.0.7), readr, readxl, rlang, scales, sctransform, sfsmisc, sf, sp, spaMM, spdep, stats, stringr, tibble, tidyr, utils, uwot, wordspace
LinkingTo:
Suggests:
curl, geoR, ggpubr, httr, janitor, kableExtra, knitr, msigdbr, progress, rmarkdown, rpart, R.utils, scSpatialSIM, spatstat, SeuratObject, tidyverse, testthat (≥ 3.0.0)
Published:
2025-06-04
DOI:
10.32614/CRAN.package.spatialGE
Author:
Oscar Ospina 
[aut, cre], Alex Soupir [aut], Brooke Fridley [aut], Satija Lab [cph] (Copyright holder of code fragments from Seurat function FindVariableFeatures)
Maintainer:
Oscar Ospina <oscar.ospina at jhmi.edu>
License:
MIT + file
Copyright:
ins/COPYRIGHT
NeedsCompilation:
yes
Materials:
CRAN checks: