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.
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
Suggests:
curl,
geoR,
ggpubr,
httr,
janitor,
kableExtra,
knitr,
msigdbr,
progress,
rmarkdown,
rpart,
R.utils,
scSpatialSIM,
spatstat,
SeuratObject,
tidyverse,
testthat (≥ 3.0.0)
Published:
2025年06月04日
Author:
Oscar Ospina
ORCID iD
[aut, cre],
Alex Soupir
ORCID iD [aut],
Brooke Fridley
ORCID iD
[aut],
Satija Lab [cph] (Copyright holder of code fragments from Seurat
function FindVariableFeatures)
Maintainer:
Oscar Ospina <oscar.ospina at jhmi.edu>
Copyright:
ins/COPYRIGHT
NeedsCompilation:
yes
Documentation:
Downloads:
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