Guides & Tutorials

In addition to the blog posts on the site, we are compiling larger, end-to-end guides and tutorials show you how to weave these tools together in your analyses.

Quarto Book: A Guide to Whole Transcriptome CosMx^® SMI Analysis

This is an end-to-end workflow that walks through analyzing a publicly-available WTX single slide dataset – from loading flat files to quality processing to performing Pathway analysis – using open-sourced tools in a blend of R and python. In here you will find best practices, interactive visualizations to show what effects certain processing parameters have on the data, and applications to cutting-edge tools that have described in our blog like HieraType.

If you want to see additional guides, please let us know on github by creating an issue with the tag “guides”.