CCC conditions sections

[cesarogiul]

Dear Daniel and Lukas Hemos,

Thank you for the nice CCC chapter - it provides a great introduction to the topic. One aspect we noticed (and already discussed with @dbdimitrov) is that the chapter doesn't directly address an issue that's becoming increasingly important as atlases keep growing in sample numbers. Specifically, how to identify cell-cell communication interactions that change across samples or conditions.

So, we are proposing to include a variety of tools in the chapter, including CrossTalkeR (https://pycrosstalker.readthedocs.io/en/stable/), scSeqCommDiff (https://gitlab.com/sysbiobig/scseqcomm), LIANA+, tensor-cell2cell/MOFA (https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html), scAccordion(https://scaccordion.readthedocs.io/en/latest/), and MultiNicheNet (https://github.com/saeyslab/multinichenetr).

We have already reached out to or plan to reach out to the authors of the tools.

We plan to make use of the already available tutorials in these tools, along with material from our recent review (https://academic.oup.com/bib/article/26/3/bbaf280/8169297?login=true) on the current state of CCC tools, as well as a tutorial we gave at ECCB 2025 (https://gitlab.com/sysbiobig/ismb-eccb-2025-tutorial-vt3).

This is the proposed structure of the differential CCC chapter:
22.1 - Approaches
22.2 - Condition-based differential cell-cell communication
22.2.1 Intercellular communication
CrossTalkeR
Liana+
22.2.2 Intracellular communication
scSeqCommDiff
multiNicheNet
22.3 - Sample Level
tensor-cell2cell
scACCorDiON
22.4 Key Takeaways
22.5 Quiz
22.6 Contributions
22.7 Session Info
22.8 References

What are your thoughts about it @Zethson?

Happy to chat more about it
Best Giulia, Vanessa @vckraemer, and James @jsnagai

[dbdimitrov]

I'd be happy to review the chapter.

If we decide to go for it, I/we can reach out also to Tensor-cell2cell as well as the MultiNicheNet teams for review/contributioms.

Suoqin Jin (CellChat first author) / Qing Nie might also be interested 🙂

[Zethson]

Dear everyone,

first of all I'm sorry for not having gotten back to you in #383 still but I just have so much on my plate that bigger efforts can take more time.

Specifically, how to identify cell-cell communication interactions that change across samples or conditions.

I totally agree, this is missing and useful. I'm not sure whether this should be included in the existing CCC chapter (which I'm still open to get overhauled by you!) or in its own chapter which would be present in "dealing with conditions". It depends a bit on the length and complexity. WDYT?

So, we are proposing to include a variety of tools in the chapter, including CrossTalkeR (https://pycrosstalker.readthedocs.io/en/stable/), scSeqCommDiff (https://gitlab.com/sysbiobig/scseqcomm), LIANA+, tensor-cell2cell/MOFA (https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html), scAccordion(https://scaccordion.readthedocs.io/en/latest/), and MultiNicheNet (https://github.com/saeyslab/multinichenetr).

I'd be happy if we could minimize the number of tools that are used in the chapter. Every tool we include adds more complexity and we need to be sure that it will be maintained for a while. Otherwise, we're just showing tech debt. Also, ideally there are benchmarks for some of these methods. Can we reduce this to maybe LIANA+ and MultiNicheNet or so? WDYT?

Let's discuss this first and then I can give you a few more technical pointers to make it work.

Thank you very much for reaching out and volunteering to contribute!

[jsnagai]

@Zethson, thank you for the quick reply and the suggestions.

I think we could reduce the tools; there are quite a lot. Maybe then we could include other tools besides those already in the current CCC chapter. This would be of extreme value for the approaches we (@vckraemer and @cesarogiul) developed and maintain.

We happy to maybe discuss and clarify our thoughts in a meeting, if you think it is useful.

Best

[Zethson]

Yeah, let's do it! Could you please reach out to me on https://scverse.zulipchat.com/? Then we can find a date & time.