This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

SpatialOmicsOverlay

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 (3.18)

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")):

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpatialOmicsOverlay")

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

Documentation

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

browseVignettes("SpatialOmicsOverlay")
Introduction to SpatialOmicsOverlay HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization
Version 1.1.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
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
Linking To
Suggests knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SpatialOmicsOverlay_1.1.0.tar.gz
Windows Binary SpatialOmicsOverlay_1.1.0.zip
macOS Binary (x86_64) SpatialOmicsOverlay_1.1.0.tgz
macOS Binary (arm64) SpatialOmicsOverlay_1.1.0.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