I am very interested to get the community's view on the best methods for identifying genes that vary over pseudotime and also modules of genes that covary over pseudotime.
I have used both the Slingshot and SCORPIUS approaches to look at T cell activation trajectories. However, I am interested in identifying the genes that vary over pseudotime, and in particular in identifying modules of genes that vary over pseudotime. I see some genes are that are activated early in the pseudotime pathway and others later, and I would like to group these into relevant modules.
I am aware of the module identification approaches available in Monocle3 and SCORPIUS and have tested both of these. However I find that they give very different results. I was wondering whether anyone has done a comparison of different gene module identification methods for time courses, and whether there is any literature out there on this?
Many thanks in advance for your thoughts and input.