automatic clustering annotation using python

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9 months ago

safeassli • 0

Hello,

I'm currently working on single-cell data processing using scanpy. After determining the clusters, the next step is cluster annotation. My question is: Is there a Python tool that allows for automatic cluster annotation, similar to SingleR in R? I'm specifically looking for a Python equivalent to SingleR.

thanks in advance

automatic-clustering single-cell • 537 views

ADD COMMENT • link updated 9 months ago by Nitin Narwade ★ 1.6k • written 9 months ago by safeassli • 0

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A simple Google search led me to this beautiful package,

https://decoupler-py.readthedocs.io/en/latest/notebooks/cell_annotation.html

Additionally, if would like to use SingleR you can use rpy2 package and run it in a Python environment. This eBook from Fabian's lab is an excellent resource if you are working with single-cell data analysis using Scanpy. I would highly recommend you go through it.