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theislab / dca

Deep count autoencoder for denoising scRNA-seq data
Apache License 2.0
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ImportError: cannot import name 'stacked_violin' #42

Closed chenziyi closed 3 years ago

chenziyi commented 4 years ago

I just install it with pip3 install dca in python 3.6.2. Then run it with a commandline "dca GSM3892344.expres.ensemble.csv ./test". ImportError: cannot import name 'stacked_violin' Could you please whether this is because the scanpy version not compatible with the dca installed here.

lylamha commented 4 years ago

I had the same issue. Basically, I had to downgrade scanpy to version 1.5.1 with pip install --upgrade scanpy==1.5.1. Then I had issues with tensorflow and keras. At the end I use tensorflow version 1.15 and keras version 2.3.0 and it works now.

chenziyi commented 4 years ago

Thanks for your kindly reply.

a-munoz-rojas commented 3 years ago

Also had the same issue. It seems that the problem is due to importing scanpy the "old way": In the dca/api.py file, line4: import scanpy.api as sc

Should be using import scanpy as sc