Monocle3 transition to seurat

Question

[odi]

I know to transition from Seurat to monocle3 one has to use library(Seurat Wrappers) and then use the function: as.cell_data_set(seuratobject).

But, after reclustering in monocle3, i would like to go back to Seurat to perform differential analysis. How do i do this?

How do i convert monocle3 object back to seurat object?

Answer 1

[antonioggsousa]

Hi,

An easy work around is just to transfer the cluster labels to Seurat meta data and continue the DE analysis in Seurat.

I don't know the structure of your data neither I'm very familiar with Monocle3, but something like this should work:

seu[["cluster"]] <- colData(cds)[,"cluster", drop=TRUE]

Where seu is your Seurat object and cds your Monocle3-related object. Cluster labels should be stored in the cell_metadata which I think you should be able to access with colData(). Apart from clusters, I believe Monocle3 gives you partition according to: https://cole-trapnell-lab.github.io/monocle3/docs/clustering/ You can follow the same code and use instead of cluster the column variable partition.

I hope this helps,

António