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MARMOT is an R-based analysis script that helps you generate publication-ready figures from your flow cytometry data — with minimal coding effort (because you've got better things to do, right? 💫).
If anything is missing, unclear, or in need of a better explanation, let us know! We’ll keep updating this wiki step by step.
The Marmots 🏔️ 🇨🇭
Please refer to this and this page for some tips and tricks about getting your data from FlowJo to MARMOT
What you'll find here:
- Exporting your .fcs files from FlowJo (because nothing's worse than starting with the wrong files 🍷)
- Filling in the metadata sheet without falling into the trap of typos or other small but highly annoying mistakes
If you struggle to open the app check out this or this page.
What you'll find here:
- A guide through the jungle of terms like UMAP, t-SNE… and wait, what was FlowAI again?
👉 Take a look at this+this+this+this pages to see the marmots' favourite DR and clustering algorithms and other options.
👉 To learn more about the internal fallback implementations included in MARMOT (e.g. Mparc, Mpacmap, Mphenograph), see the this page.
You'll find general recommendations for designing experiments with MARMOT. These guidelines are based on our own experiences and should be adapted to your specific needs – they are not set in stone. 🪨
Lastly, please take a moment to include some of these key references in your work if you've used MARMOT