In this repository I thought it would be a fun project to go through the Nanostring CosMx SMI data. Here, we will be using the human frontal cortex dataset that uses their upgraded 6000-plex technology. This is part of a series on Youtube.
- My first video was talking a little bit about spatial transcriptomics and downloading the dataset here.
- Second video is exploring the Seurat object and looking at some of the resolutions that we have (slide, field of view, cellular) here
- Cleaning the Seurat object, running normalization, PCA/UMAP, and clustering here