Merged loop calls with contact frequency from replicate Hi-C experiments

Using data from "Phase separation drives aberrant chromatin looping and cancer development" by Ahn et al. 2021 (GEO links GSE143465 and GSE143465), looping interactions were called with SIP (https://github.com/PouletAxel/SIP). Resulting loop calls were merged using functions from `hictoolsr` and interactions were extracted from replicate `.hic` files. The resulting file can be used to demonstrate differential loop calling between two biological conditions.

data("loopCounts")

Format

a GInteractions object with metadata columns describing loop properties and interaction counts from replicate Hi-C data

References

Ahn, Jeong Hyun, Eric S. Davis, Timothy A. Daugird, Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li, et al. 2021. “Phase Separation Drives Aberrant Chromatin Looping and Cancer Development.” Nature 595 (7868): 591–95.

SIP (https://github.com/PouletAxel/SIP)