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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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How to transform csv files to be used with Azimuth #3606

Closed algebio closed 3 years ago

algebio commented 3 years ago

Hi

I can export csv files from SeqGeq and I would like to use them with Azimuth but I have to transform them. Azimuth only accepts the following formats:

Seurat objects as RDS 10x Genomics H5 H5AD H5Seurat Matrix/matrix/data.frame as RDS

So I have two questions: Which is the best csv option to export from SeqGeq? How can I transform the csv file so I can use it in https://satijalab.org/azimuth/?

Regards Juan

cdarby commented 3 years ago

Thanks for your interest in Azimuth! I am not familiar with SeqGeq, but you'll need a counts matrix. This is what Azimuth starts from. Read the CSV file into R. You can use a matrix or a data.frame. Ensure that the row names are genes and the column names are cell names - the first row and/or first column should NOT be the names. Save this object as an RDS and upload.

algebio commented 3 years ago

Thank you cdarby 👍