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: |
1.2.0 |
| 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: |
geoR, ggpubr, janitor, kableExtra, knitr, msigdbr, progress, rmarkdown, rpart, R.utils, scSpatialSIM, spatstat, SeuratObject, tidyverse, testthat (≥ 3.0.0) |
| Published: |
2025-05-13 |
| 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 [issues need fixing before 2025-05-27] |