G4Damage

Pipeline for cross mapping DNA damage with regard to G-quadruplex structures.

DNA damages from various context are mapped onto G4 stuctures with varied stability. The damage propensity is plotted and discussed in detail in the publication.

Workflow to get similar plots in the publication

Change the variables as follow:

1. UV damage plots
   dmg.names = c('CPD', 'PP')
   dmg.type = "UV"
   dmg.pattern = c("CT", "TC", "TT")
   strand.sensitive = T
   combine.plot = F
2. cisplatin damage
   dmg.names = "cisplatin"
   dmg.type = "cisplatin"
   dmg.pattern = "GG"
   strand.sensitive = T
3. 8oxoG damage
   dmg.names = "oxoG"
   dmg.type = "oxoG"
   dmg.pattern = "G"
   strand.sensitive = T
4. breakage damage
   dmg.names = c("sonication", "enzymatic", "ancient")
   dmg.type = "breakage"
   dmg.pattern = "NN"
   strand.sensitive = F
   combine.plot = T