GOEA as in the jupyter notebook with my own files

tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms

BSD 2-Clause "Simplified" License

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GOEA as in the jupyter notebook with my own files #205

Closed ziphra closed 2 years ago

ziphra commented 3 years ago

Hello,

I would like to know how could I run a gene ontology enrichment analysis with my own files using a python IDE following your example from the Jupiter notebook (without downloading associations or background gene sets from NCBI, as in the example). I am not sure I get all the requirements to do so.

Thank you!

tanghaibao commented 3 years ago

@ziphra

Sorry for a late response ... not sure if you are still stuck on this one but the Jupyter notebook is no different from a Python IDE. There is no magic to download separate files and goatools automates some of the downloading as well.

Would you point to which notebook that you are interested in running in a Python IDE but couldn't run due to missing datasets?

algogalo commented 3 years ago

Hi there @ziphra,

I replied to another issue that might be similar

https://github.com/tanghaibao/goatools/issues/113#issuecomment-880779873

I hope this helps.