Real-time integration

[Marius1311]

• Additional function parameters, change functionality or change defaults?
• New estimator in cr.tl.estimators?
• New kernel in cr.tl.kernels?
• New gene trend model in cr.ul.models?
• New plotting function in cr.pl?
• Other?

This is about including a kernel that computes a directed transition matrix base on real-time information. Some options that come to my mind:

• WaddingtonOT [WOT] (pairwise unbalanced optimal transport among time-points), see https://www.cell.com/cell/pdf/S0092-8674(19)30039-X.pdf
• global Waddington OT [gWOT] (same as WOT, but OT problem solved simultaneously for all time points rather than pairwise), see https://github.com/zsteve/gWOT
• Dana's harmony (heuristic that uses mutual nearested neighbors in conjunction with regression to estimate the existence and strength of inter-timepoint links), see https://www.nature.com/articles/s41586-019-1127-1 or https://github.com/dpeerlab/Harmony

These are just three, there are probably more out there. Architecture-wise, it would probably make most sense to include this via the external interface.

[Marius1311]

We have decided to integrate WOT. @michalk8, are there any news here?

[michalk8]

closed via #595