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: | Rcpp, RcppEigen, RcppProgress |
| 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 LICENSE |
| Copyright: | ins/COPYRIGHT |
| NeedsCompilation: | yes |
| Materials: | README, NEWS |
| CRAN checks: | spatialGE results |