Figure2.Rmd - recreates majority of Figure 2 (Shh regulatory domain) from the manuscript - interaction matrix generated by FANC added later and edited in Illustrator

Figure3.Rmd - recreates majority of Figure 3 (Irx3 regulatory domain) from the manuscript - interaction matrix generated by FANC added later and edited in Illustrator

Figure4.Rmd - recreates Figure 4 (PPV of heuristics), which was later edited in Illustrator

Misc.Rmd - pieces of code to compute distances and nearest genes for various sections of the manuscript