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greenelab / core-accessory-interactome

Investigating the functional relationship between P. aeruginosa core and accessory genes.
BSD 3-Clause "New" or "Revised" License
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Lookup samples for Georgia's manuscript #38

Closed ajlee21 closed 3 years ago

ajlee21 commented 3 years ago

The main change in this PR is looking up samples that have high PAO1 and PA14 accessory expression for Georgia's manuscript: explore_data/samples_with_mixed_acc_expression.ipynb

There are some minor updates to existing notebooks to make sure the runs were reproducible with some of the past changes. This PR also updated the readme to make sure it is consistent with the most current pipeline

ajlee21 commented 3 years ago

LGTM! Is there a python script for 1. processing/1_create_compendia.ipynb?

There is a python script. I'm not sure why it didn't sync. Good catch.

Interesting on that some of the samples are for wound infections. This leads me to ask: Does psudeomonas affect wounds? Probably should know this information, but asking anyway.

Yes, along with Staphylococcus aureus, Pseudomonas aeuginosa is also commonly found in wound infections.