Progress updates, SPAMO, and more

TODO Show GREAT figure [1/2]

• Looks good, but need to check GO slim

TODO Talk to Lee about GO Slim

• I need a GMT file, can be from a URL
• Can be done by intersecting, than recomputing FDR (False discovery rate)
• Use Generic GO subset https://geneontology.org/docs/go-subset-guide/
• Can try to convert OWL to GSEA GMT gene set

DONE Ask about merging bed files

• Note taken on [2025-06-06 Fri 10:20]
  - Intervene generates bed file sets (upset plot)
  • In old_analysis directory
  • Molly will send us code
• Just bedtools merge?
• Need to Make the 7 or 8 merge (how is this different than merging 8?)

DONE SPAMO?

• Note taken on [2025-06-06 Fri 10:07]
  Matt wants to go in a different direction, but molly is taking care of it
• I need to send to matt right?
• May not be relevant

DONE Next week's agenda

• Note taken on [2025-06-06 Fri 10:10]
  Wait until Shreeja Gets back for Phenotype RELI

DONE Methods Wiki page (is this a good place for draft methods?)

• Note taken on [2025-06-06 Fri 10:09]
  Wiki is a good forum
• Subpage of PU.1