Guides & Tutorials

Guides & Tutorials 📚

End-to-End Analysis Workflows

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

Available Guides

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 been described in our blog like HieraType.

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Want to see a specific workflow?

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

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