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Matrix construction between CellRangerRkit, Seurat, and Monocle

Posted By: rmtsoa, on Sep 15, 2017 at 11:23 AM

Hi:

 

I just finished clustering analysis using Seurat. I got cluster composition and top differentially expressed genes. Now, I am trying to feed in this matrix to Monocle psudotime analysis. However, I have some issues about CDS construction for Monocle. Does anyone already have the workflow worked out?

 

Thanks,

Rosemarie

2 Replies

Re: Matrix construction between CellRangerRkit, Seurat, and Monocle

Posted By: paulr, on Sep 22, 2017 at 8:03 PM

In case anyone is interested or has similar problems, there's more info on the Monocle github issues page here:

https://github.com/cole-trapnell-lab/monocle-release/issues/24

Re: Matrix construction between CellRangerRkit, Seurat, and Monocle

Posted By: rbg, on Feb 6, 2018 at 8:01 AM

Hi,

Did you find the solution for this?

I am looking to do same using importCDS(seuratObject), but were you able to use 

plot_cell_trajectory() on the seurat converted monocle object

please let me know, how you proceeded.

thanks!

rbg.