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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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Add enrichment analysis of modules #40

Closed ajlee21 closed 3 years ago

ajlee21 commented 3 years ago

This PR is updating a few different analyses:

  1. Add KEGG pathway enrichment to find acc-acc modules that have an over-representation of some KEGG pathway. (acc_acc_analysis/1_annotate_acc_modules.ipynb)
  2. Look for which KEGG pathways the most and least stable core genes are found to be associated (core_core_analysis/2_find_KEGG_associations.ipynb)
  3. Find which genes the most and least stable core genes are related to (core_acc_analysis/stable_gene_relationships.ipynb)
nrosed commented 3 years ago

Looks good! no major comments from me, everything seems clear and straightforward. 👍🏼