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saezlab / visium_heart

Spatial transcriptomics of heart tissue
GNU General Public License v3.0
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incomplete contents in your convert_rds_to_h5ad_visium.ipynb file #15

Open howtofindme opened 1 year ago

howtofindme commented 1 year ago

Hi, excellent work! Congratulations!

I am learning from your scripts, could you kindly offer the complete codes in this file?

best, Young

image

lzj1769 commented 1 year ago

Hi,

You can check this file https://github.com/saezlab/visium_heart/blob/master/cellxgene_submission/convert_rds_to_h5ad_snATAC.ipynb

Basically, they are doing the same job, i.e., converting a Seurat object to an h5ad file.

howtofindme commented 12 months ago

Hi,

You can check this file https://github.com/saezlab/visium_heart/blob/master/cellxgene_submission/convert_rds_to_h5ad_snATAC.ipynb

Basically, they are doing the same job, i.e., converting a Seurat object to an h5ad file.

Thanks for your timely reply.

I have tried many times as you mentioned. It works for sc/snRNA data. but it does not work for spatial data. I guess it might be caused by the images stored in seurat object. because SaveH5Seurat and Convert functions do not process the image data.

Is it possible that you could give me an example on how to convert rds to h5ad_visium?

best wishes, Young