gravatar for Bogdan

2 hours ago by

Palo Alto, CA, USA

Dear all,

referring to scRNA-seq analysis and Monocle3 trajectory reconstruction in pseudotime
(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

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