Include more options for niche definitions

[timtreis]

Currently, squidpy focusses mostly on local spatial neighborhoods for niche analysis purposes. However, there are other definitions which one could use. Including other options could increase tool usage and enable other usecases, f.e. nische-detection-robustness testing?

Pinging @melonora @LLehner @MohammedZidane

[timtreis]

Hey @LLehner, let's discuss the feature in this issue. Here there's the monkeybread package that we mentioned during the meeting: https://monkeybread.readthedocs.io/en/latest/

[LLehner]

Neighborhood based:

• monkeybread (clustering of neighborhood profiles)
• CellCharter (performs dimreduction, neighborhood calculation, aggregation and clustering)
• UTAG

VI and Bayesian methods:

• DestVI ("Unlike other methods, DestVI learns both discrete cell-type-specific profiles and continuous sub-cell-type latent variations using a conditional deep generative model")
• BayesSpace

OT-based:

• SPOT (Cluster cells based on their niche similarity, not their expression similarity)

MRF-based:

• DR-SC

GRN based:

• NicheHotSpotter ("NicheHotSpotter calculates the probability that a signalling node participates in niche–stem cell signalling from the stationary distribution of a finite discrete time-homogenous Markov chain model")

Cell-Cell-Communiation based:
One could reason about niches by analyzing cellular interactions:

• CellPhoneDB
• NicheNet
• NCEM

pre-trained (foundational) models:
Perhaps one could utlize pre-trained (foundational) models to predict niches.

• Nicheformer
• STAGATE

[timtreis]

Amazing, thank you! Could you also briefly look into the respective requirements? Ideally I'd hope that there is a small subset that we can add without adding to our dependencies (core) and the other methods will complain about their specific solvers or whatever not being installed when they're called (addon).

Then we could start with the core methods and also merge them without adding to the dependency load of the base package before things are evaluated and stable and later on cast the addon ones into the template we talked about