With respect to the manuscript
Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, and Ferhat Ay, Identification of significant chromatin contacts from HiChIP data by FitHiChIP, Nature Communications, Vol 10, No 4221, 2019, DOI: https://doi.org/10.1038/s41467-019-11950-y
Here is the link of various utility scripts used in the paper:
https://github.com/ay-lab/Utilities/tree/main/APA
https://github.com/ay-lab/Utilities/tree/main/Loop_CTCF_Orientation
https://github.com/ay-lab/Utilities/tree/main/Loop_Overlap_Venn
https://github.com/ay-lab/Utilities/tree/main/Recovery_Plot_FitHiChIP
https://github.com/ay-lab/Utilities/tree/main/Recovery_Plot_1D_Peaks