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ktrns / scrnaseq

Workflow for single-cell RNA-seq analysis using Seurat
MIT License
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Pseudotime analysis #46

Open ktrns opened 4 years ago

ktrns commented 4 years ago

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.

ktrns commented 3 years ago

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

ktrns commented 3 years ago

I think that we should look into Cell Rank.

However, not for release 1.0 :-), it can come in later.

kosankem commented 2 years ago

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