scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics

Question

[Bogdan]

Dear all,

referring to scRNA-seq analysis and Monocle3 trajectory reconstruction in pseudotime (https://cole-trapnell-lab.github.io/monocle3/) :

we have 10 samples, and Monocle3 successfully infer the trajectories, however the number of genes that are Diff Expressed along the pseudotime is huge (ie > 4000 genes; we are working with 5 time points).

i would like to ask please : how would you filter further the list of genes that are Diff Expressed along the Pseudotime (beside p-value, q-value) in order to keep the follow the genes that are expressed in a larger fraction of cells ?

could this filtering be done based on Moran I statistics only (or, alternatively, i shall write additional scripts that count the number of expressing cells of gene 1, gene 2, gene 3, etc ) ?

thank you,

-- bogdan

[VolEr]

Hi Bogdan,

I have a similar issue struggling with, I am wondering if you were able to find a way to filter DE genes showing a smooth change across samples.

Best V

[Bogdan]

Hi :

i 'd think that one way would be to filter based on the number of counts per GENE at the beginning and end of the trajectory;

i have started to look a while ago into TradeSeq (https://github.com/statOmics/tradeSeq) that has good documentation :)

[VolEr]

Thanks, I'll look through it.