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BIMSBbioinfo / ikarus

Identifying tumor cells at the single-cell level using machine learning
MIT License
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pyscenic does not contain genesig #12

Closed rekado closed 2 years ago

rekado commented 2 years ago

The latest release of pySCENIC no longer provides pyscenic.genesig:

https://github.com/aertslab/pySCENIC/commit/a137cd16bbbb327d56d2a4e9d454c7b316199437

This has moved to ctxcore.

rekado commented 2 years ago

FWIW I added python-ikarus to Guix with commit 81cf674a5d5e3dc020df5d43ce62e1c98f2c9711. The package includes a fix for this issue.

erevkov commented 2 years ago

Hi! I wanted to try using the package, but after installing I ran into the same error: ModuleNotFoundError: No module named 'pyscenic.genesig' (Python 3.8, installed with pip+git in a conda environment). Will there be a fix anytime soon, or perhaps there is a fixed version available elsewhere already?

rekado commented 2 years ago

@erevkov in the meantime you can patch this by replacing "pyscenic.genesig" with "ctxcore.genesig" in ikarus/classifier.py.

dohmjan commented 2 years ago

Hi! Thank you for the hint, it's now also changed in the repo.

melonheader commented 2 years ago

@erevkov Could you tell if the model works for you after the update?

erevkov commented 2 years ago

Yep, looks like this is working now, thanks!