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This is the development version of standR; for the stable release version, see standR.

Spatial transcriptome analyses of Nanostring's DSP data in R

Bioconductor version: Development (3.20)

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

Author: Ning Liu [aut, cre] , Dharmesh D Bhuva [aut] , Ahmed Mohamed [aut]

Maintainer: Ning Liu <liu.n at>

Citation (from within R, enter citation("standR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

standR_introduction HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports dplyr, SpatialExperiment(>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
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Suggests knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package standR_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64) standR_1.9.0.tgz
macOS Binary (arm64) standR_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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