TODO Create UMAP and PCA (Part B) [2/3]

• Molly made the samplesheets manually so need to regenerate with code to add more metadata columns
• Matt wants supplemental figures for antibody and experiment
• Antibody already has label, but need experiment annotations
• [X] Antibody supplement
• [X] Set colors to match cell type diagram

Figure 2

TODO GREAT analysis (Part D) [1/4]

• In the Figures folder
• Where did bed files come from?
• [X] Emailed Lee about code
• Use fold enrichment instead of odds ratio
• Generate Tables
• Integrate great script with makefile?

Figure 3

TODO Part A-B

• Move SPI1/ets to bottom of bar plot

TODO SPAMO analysis (Part C)

• Identifies likely partners for PU.1
• May or may not be working on it?

Figure 4

TODO Phenotype RELI (Part A)

• Needs new GWAS catalogue
• Leah Released GWAS catalogue (how do I get it?)

Shreeja is the GWAS gatekeeper.

– Matt

TODO Mario Analysis

• Identifies allele dependant behavior

TODO Download EGA datasets (vcf files)

• Required for MARIO analysis
• Need Permission still (shreeja will know)

DONE Draft Methods

-Note taken on [2025-06-03 Tue 13:06]
Added to wiki at https://tfwiki.cchmc.org/wiki/PU.1_Project/Methods

• Put in Docs folder
• Maybe put on wiki instead?

Papers to Read

TODO Harley et al

Want to, but don't need to?

TODO Dockerize/Nixify R dependencies

• Are we publishing code?