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

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Bioconductor version: Development (3.19)

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>

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


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:

Introduction to SpatialOmicsOverlay HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization
Version 1.3.1
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
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Suggests knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf
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Follow Installation instructions to use this package in your R session.

Source Package SpatialOmicsOverlay_1.3.1.tar.gz
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macOS Binary (x86_64) SpatialOmicsOverlay_1.3.1.tgz
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Source Repository (Developer Access) git clone
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