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How to convert h5ad object to rds object without raw counts?

How to convert h5ad object to rds object without raw counts?

h5ad
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updated by yura.grabovska • yura.grabovska • written by hejenny792 • hejenny792

Can you please give more information on what you'd like to do?

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written by yura.grabovska • yura.grabovska

I downloaded both log2 and "raw" objects from Allen Institute (https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/WMB-10Xv3/20230630/) and tried to convert the h5ad object to rds to do reference mapping because I couldn't find a good package in Python (if you could recommend a good one in Python, I would appreciate that). The problem is that I can't find row counts from both h5ad files. I wondered if there was a way to convert it without raw counts. Any suggestions are appreciated. Thanks!

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written by hejenny792 • hejenny792

Hi, unless I am missing something, an RDS object in R is just a data storage format - it's an object from the R environment which is compressed and stored and can then be retrieved later.

Since you're working with 10x data I assume you want to convert h5ad to a format that can be read into Seurat?

In that case you can look at the example here

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written by yura.grabovska • yura.grabovska

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