Find differentially expressed genes at branchpoints which decide cell fates

[gilstel]

The tutorial section entitled "Finding genes that change as a function of pseudotime" helps to find which genes change using pseudotime, but all over the graph. When I tried this approach I received thousands of genes and when I filtered for a low q-score I still got hundreds of genes. I also added filtration using a high Moran_I score but the top scoring genes were all over the graph and I could not find a way to isolate genes near branchpoints of annotated cell types. I would like to know what genes change between certain branchpoints. For example, which genes drive the changes between branchpoint 3 and 5 or only in 9 in the following graph -

The tutorial section entitled "Analyzing branches in single-cell trajectories" enables interactively selecting cells in order to find DE genes within them.

Since branchpoints were already defined, I would like to use them in order to understand the cellular decisions that are being made. I would like to use all branchpoints programmatically without the need to select the cells each time.

What is the best way to answer the question which genes govern the decisions at each branchpoint?

Many thanks for your help

[aanchalsharma833]

@gilstel , were you able to figure out a solution for this problem?

[gilstel]

Unfortunately not I gave up