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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

3 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.

Re: Matrix construction between CellRangerRkit, Seurat, and Monocle

Posted By: mstreube, on Mar 14, 2018 at 5:47 AM

Hi all,

 

I am also trying to work with Seurat data in Monocle.

Have somebody managed to do this???

 

>What I found out so far was that one first has to load the workspace (".RData") into your environment:

 

You can do this with clicking the button in the right upper window or R under "Environment" or use the command below:

load("storage_place/name_of_your_workspace.RData")

 

>In the next step you have to use the following command to import your Seurat data:

importCDS(name_of_your_Seurat_object_you_used_before, import_all = TRUE)				

 

Now I am sticking in the next step, because no matter what I do there are only errors, which tells me:

unable to find an inherited method for function ‘exprs’ for signature ‘"seurat"’

Did I miss something? Does somebody have an idea how to go on from here?

 

Thank you very much in advance,

Michael