PU1-meeting-12-01-2025

  • Data is in DBGap
  • Will be hard to submit to GEO
  • Het list

PBM predictions (figure 5 scatter plots)

  • Matt will Pick the Motif after fixing his program
  • Then send to Xioating to rerun

Figure 5

  • scatter plots need to be Squares
  • R should be title

Figure 6

  • Figure out score cutoff for alphagenome
  • SNPmoods score cutoff

Supplementary information

supplementary figure 1 (umaps)

  • Get GSM experiment ID for all GEO studies (Rename title to "Study") 
BiocManager::install("GEOquery")

library(GEOquery)

gsm_to_gse <- function(gsm_id) {
  gsm <- getGEO(gsm_id, destdir = tempdir())
  Meta(gsm)[["series_id"]]  # This usually gives GSE IDs
}

gsm_to_gse("GSM1010843")
  • Output version with no legend for lucinda
  • Peak bins should be round numbers

Absolute number of specific peaks is driven by number of datasets

TODO Ellie Kim has Mario/RELI/HOMER README files (Excel)

  • [X] I should email them and ask for these
  • Make wiki articles

Figure 1 supplemental

Need to regenerate figures without legends