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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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Minor refactor #45

Closed ajlee21 closed 3 years ago

ajlee21 commented 3 years ago

This PR makes a few minor refactors. These changes include:

  1. Adding documentation about the raw dataset that we use, that is described in another repo (1_processing/README.md)
  2. Re-ordering directories since the common DEGs analysis depends on the core-core analysis
  3. Remove PAO1 gene ids that were found in the PA14 compendium (1_processing/0_format_expression_data.ipynb)

Many files are changed because I made sure all the notebook ran successfully, but the main ones to look at are listed above

ajlee21 commented 3 years ago

Looks good to me! You're right, most of the changes were pretty straightforward. One thing to note is that 2_correlation_analysis/1_correlation_analysis.ipynb wouldn't let me see the changes, so it was hard for me to see if there was anything that needed addressing there, but I'm sure it's fine.

Thank you for taking a look. This notebook displays some pretty large correlation plots so I'm not sure if there was an issue loading the notebook, but seems to work for me. This one shouldn't have had code changes in them though