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kashyapchhatbar / eme_selex

BSD 3-Clause "New" or "Revised" License
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Issue on page /workflow.html #1

Closed dktanwar closed 2 months ago

dktanwar commented 1 year ago

I am trying to reproduce the notebook.

I guess, I can download the data from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-9236

But, I would like to have "data/metadata.tsv" file. I.would be great if you could please provide this file, so that I can run the notebook with minimal efforts.

Thank you very much.

dktanwar commented 1 year ago

I found this file, but still the notebook is not reproducible.

kashyapchhatbar commented 1 year ago

Hi @dktanwar,

Thanks for getting in touch. Apologies for not replying sooner. Can you send some more information about the error?

Best, Kashyap

kashyapchhatbar commented 1 year ago

I have added two minor fixes which were related to pandas. These changes are necessary since pandas are handling some defaults in a different way.

Can you let me know if following these steps help?

Clone the repository

git clone https://github.com/kashyapchhatbar/eme_selex.git

Navigate in the docs directory

cd eme_selex/docs

Make sure you have all the python packages

Follow this link https://eme-selex.readthedocs.io/en/latest/workflow.html#before-you-begin for more information

When you run the Notebook.ipynb in Jupyter, the notebook shouldn't throw any error. Please let me know if it doesn't work.

Many thanks, Kashyap