ktrns
Pseudotime analysis
It would be great to extend the workflow with pseudotime analysis. Several customers would like to see this kind of analysis, see velocity or trajectory inference.
Katrin incorporates slingshot.
Andreas will check out velocity analysis, and incorporate it if it is an easy fix. Else we keep it for later. https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/velocity.html
I think that we should look into Cell Rank.
However, not for release 1.0 :-), it can come in later.
For one of our project I have put together a small R markdown script which is using the output of the scrna script and performs some pseudotime analysis and cell trajectory. Hence, this small script (i called it pseudotime_monocle) is easily to run subsequently to the main script. The pseudotime analysis is performed via monocle3. That means, in the process I converted between Seurat S4 - SingleCellExperiment - S4 object. I am not sure that this is the nicest solution, but so far it seems to work. I am looking for more dataset for a more thoroughly testing, though. However, in case you are interested in it, you can find it in our repository under https://github.com/MHH-RCUG/scrnaseq/tree/Additional-scripts
