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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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counts matrix cannot be imported into spyder using io.mmread function #8705

Closed yulchen810 closed 6 months ago

yulchen810 commented 6 months ago

Hi, I'm trying to do RNA velocity analysis in python. I have already installed scvelo and other relevant packages in conda (python version 3.9). I extracted count matrix using following code in R:

counts_matrix <- GetAssayData(seurat_obj, assay='RNA', slot='counts')

Now, there is an error when I import matrix to spyder using io.mmread function 截图20240331222806

Does anyone know why is that? Thank you!

samuel-marsh commented 6 months ago

Hi,

This does not appear to be an issue with Seurat but on python side (or perhaps how you saved the matrix). I would suggest posting to repo for python package for help with this issue.

Best, Sam

yulchen810 commented 6 months ago

Ok, thank you for your suggestion.

Best, Xiaoyan

On Tue, Apr 2, 2024 at 8:33 PM Samuel Marsh @.***> wrote:

Closed #8705 https://github.com/satijalab/seurat/issues/8705 as completed.

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