References

We hope you've had fun using MARMOT, and more importantly, generated some exciting results for your paper!

It would be really great if you would cite MARMOT and the main packages it depends on in your publications. Please feel free to reach out to us for help writing the methods section for MARMOT and we can also help you get all the key references in.

Citations are up there with carrots as marmots' favourite treats, so thank you in advance! 🥕🦫🏔️🇨🇭

• MARMOT: Kirsche et al., 2025, https://doi.org/10.1016/j.jim.2025.113854

• CATALYST: Crowell et al., 2024, https://doi.org/doi:10.18129/B9.bioc.CATALYST

• diffcyt: Weber et al., 2019, https://doi.org/10.1038/s42003-019-0415-5

And depending on which methods you used:

• FlowSOM: Van Gassen et al., 2015, https://doi.org/10.1002/cyto.a.22625

• Phenograph: Levine et al., 2015, https://doi.org/10.1016/j.cell.2015.05.047

• FlowAI: Monaco et al., 2016, https://doi.org/10.1093/bioinformatics/btw191

... and many more