SpatialOmicsOverlay

Overview

The SpatialOmicsOverlay package contains tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP). It provides functions to extract image and XML from OME-TIFFs, overlay Regions of Interest (ROIs) onto the image, and manipulate the image (coloring, orientation, cropping). Output figures are ggplot based allowing for easy customization of images to include spatial images into data visualization.

Installation

Download the release version from Bioconductor

https://bioconductor.org/packages/release/bioc/html/SpatialOmicsOverlay.html

Install the release version from Bioconductor

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

BiocManager::install(version="release")

BiocManager::install("SpatialOmicsOverlay")

Install the development version from GitHub

install.packages("devtools")
library("devtools")
devtools::install_github("Nanostring-Biostats/SpatialOmicsOverlay", 
                         build_vignettes = TRUE, ref = "dev")

Documentation

To learn how to start using SpatialOmicsOverlay, view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpatialOmicsOverlay")

or download vignette from NanoString website (pending)

Branches

The dev branch on GitHub is under active development and no guarantee is made on usability at any given time. https://github.com/Nanostring-Biostats/SpatialOmicsOverlay

Citation

Griswold, M. SpatialOmicsOverlay: Spatial Overlay for Omic Data From Nanostring GeoMx data. R Package Version 0.99.10. NanoString Technologies Inc.; Seattle, WA 98109, USA. 2021.

License

This project is licensed under the MIT license.