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Christensen-Lab-Dartmouth / MethylNet

Modular framework for deep learning predictions on methylation data.
https://christensen-lab-dartmouth.github.io/MethylNet/
MIT License
51 stars 11 forks source link

Separate methylation processing pipeline #3

Closed AlexanderTitus closed 5 years ago

AlexanderTitus commented 5 years ago

Wrapping the methylation pipeline in Python is a great contribution to the field in itself. We should consider cleaning that into its own repo and possibly submitting an application note to Bioinformatics or at a minimum bioRxiv to let the community use that as a separate resource.

AlexanderTitus commented 5 years ago

And if we do that we should create a PyPi package for easy use. @jlevy44 we should chat about a division of labor.

jlevy44 commented 5 years ago

We can certainly discuss this. I limited the options that someone has over specific preprocessing tasks in this repo, but it would be nice to have a unified framework for running meffil, minfi, enmix, etc. through a python cli. I have this pipeline wrapped in docker and cwl.

A problem we would have to work through when taking a pypi approach is the installation of the bioconductor packages. I have prepared a custom installer object to handle these custom installations.

Nevertheless, I can go ahead and make a separate repo for preprocessing so we can develop it to a finished state.

jlevy44 commented 5 years ago

Let's continue this discussion over here: https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess

I removed the preprocessing script from this repo and moved it over to PyMethylProcess. From now on, issues submitted here should be related to workflow development, deep learning models and visualization as well as biological interpretation.