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 + fileLICENSE |
| Copyright: | ins/COPYRIGHT |
| NeedsCompilation: | yes |
| Materials: | README,NEWS |
| CRAN checks: | spatialGE results |