# 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 ``` r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(version="release") BiocManager::install("SpatialOmicsOverlay") ``` ### Install the development version from GitHub ``` r 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: ``` r 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](LICENSE).