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Spatial Overlay for Omic Data from Nanostring GeoMx Data

Bioconductor version: Release (3.18)

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Author: Maddy Griswold [cre, aut], Megan Vandenberg [ctb], Stephanie Zimmerman [ctb]

Maintainer: Maddy Griswold <mgriswold at nanostring.com>

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


To install this package, start R (version "4.3") and enter:

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


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:

Introduction to SpatialOmicsOverlay HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization
Version 1.2.1
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT
Depends R (>= 4.1.0)
Imports S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats
System Requirements
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Suggests knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SpatialOmicsOverlay_1.2.1.tar.gz
Windows Binary SpatialOmicsOverlay_1.2.1.zip (64-bit only)
macOS Binary (x86_64) SpatialOmicsOverlay_1.2.1.tgz
macOS Binary (arm64) SpatialOmicsOverlay_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpatialOmicsOverlay
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialOmicsOverlay
Bioc Package Browser https://code.bioconductor.org/browse/SpatialOmicsOverlay/
Package Short Url https://bioconductor.org/packages/SpatialOmicsOverlay/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive