SpatialOmicsOverlay WorkshopBelow are video tutorials for this GTN material, created for various (past) events.
Tutorial Video ()
This workshop will introduce users to the NanoString R package SpatialOmicsOverlay. This package is designed for use in interpretation and presentation of the multi-form data generated by NanoString’s GeoMx ® Digital Spatial Profiler spatial biology platform. The GeoMx DSP produces both rich imaging and genomics data. Integrating these data types facilitates a deep understanding of the profiled tissue. The SpatialOmicsOverlay package integrates both of these data types, thereby by maintaining the relationship between underlying tissue morphology and resultant gene expression.
Specifically, SpatialOmicsOverlay was developed to visualize and analyze the free-handed nature of Region of Interest (ROI) selection in a GeoMx experiment, as well as the immunofluorescence-guided segmentation process. The overlay from the instrument is recreated in the R environment, which allows for plotting overlays with data like ROI type or gene expression. The package provides a convenient workflow for users to generate customized, sharable visualizations.
The Introduction to SpatialOmicsOverlay vignette demonstrates how to use OME-TIFF files, which are exported from the GeoMx platform. Participants will learn how to interact with this file type and generate informative plots over images. This vignette utilizes data from our Spatial Organ Atlas. The Spatial Organ Atlas is a freely-accesible resource of whole transcriptome spatial profiles of functional components of tissues from human and mouse generated using our Whole Transcriptome Atlas RNA assay. In particular, vignette users will be analyzing data from the mouse brain. This content is similar to the vignette available with the package upon installation.
|Captions:||No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.|
How to Embed this
If your content supports iframes, you can copy this code:
<iframe src="https://gallantries.github.io/video-library/videos/bioconductor/SOOBiocWorkshop/tutorial/embed.html" width="600" height="800" allow="encrypted-media *; fullscreen *; autoplay *;">
Or if you just want the URL to embed the content