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farrellja / URD

URD - Reconstruction of Branching Developmental Trajectories
GNU General Public License v3.0
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Importing Seurat ro URD #11

Closed fereshtehizadi closed 6 years ago

fereshtehizadi commented 6 years ago

Hi,

I have clustered my cells by Seurat, now I would like to trace gene expression pattern during the development by URD. I tried to figure how how I could import my Seurat object to URD but unfortunately I failed. Could you please help me in this regard?

Thanks lot in advance

farrellja commented 6 years ago

Hi. You probably want to try the function seuratToURD. You can get more information about the function by typing ?seuratToURD. If you had a problem recently with this function, you may try reinstalling from the debug branch, as I recently updated this function to correct a bug where it would not important properly if PCA or tSNE had not been calculated in Seurat.

If you missed them, you will likely find the two guides in URD/Analyses in this repository useful as you try to apply the software, as well as the internal documentation. You can type ?URD to get a starter set of links, and the index is at the bottom that links to the documentation for all functions.