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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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Can I use bulk RNA sequencing data as reference? #32

Closed BW15061999 closed 2 years ago

BW15061999 commented 2 years ago

Hi, I have a dataset with about 100 samples and each cell type contains around 10-20 samples, can I make it as a reference dataset and project a single cell RNA dataset onto it?

Thank you!

mass-a commented 2 years ago

Hello, currently we do not have a direct way of using a bulk RNA-seq dataset as a reference.

Perhaps you could try using a tool such as singleR, which should allow you to train a classifier based on your bulk data?

Best, -m

BW15061999 commented 2 years ago

Thank you! I will give it a try.

Best