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saezlab / decoupler-py

Python package to perform enrichment analysis from omics data.
https://decoupler-py.readthedocs.io/
GNU General Public License v3.0
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ORA analysis get hung in jupyter notebook #126

Closed zhaleh-safikhani closed 1 week ago

zhaleh-safikhani commented 1 month ago

Hi @PauBadiaM, For some reasom when I run some functions from decoupler like ora in jupyter notebook, they got hung while they work fine in a python script. I use the same virtual environment in both cases and I have decoupler=1.6.0 installed in this env. Do you have any idea why that might be the case?

PauBadiaM commented 1 month ago

Hi @zhaleh-safikhani ,

Did you run it using the verbose parameter, could you tell me exactly where does it get stuck? It might be a problem of parallelization in case you are running decoupler on massive amounts of cpus, you could try to limit them by running these lines:

import numba as nb
nb.set_num_threads(n=32)

# Then run decoupler functions here