Code for Zenk, Zhan et al., Nature 2021

Content

HiC-Pro_parameters folder:

Within this folder, you find the HiC-Pro parameter file utilized for the analysis of the Hi-C data.

compartments_calling

Within this folder, you find R script together with bash utils to call local compartments instead of chromosome-wide compartments.

image_analysis

Within this folder, you find Fiji macro to calculate the distance from centre of mass and to calculate blob volumes

saddle_plots

Within this folder, you find R script together with bash utils to create saddle plots.

Simulations:

Within this folder, you find the input configurations to run genome-wide simulations in lammps (credit to Pavel Kos). You find also the specific version of MonteGrappa to run the simulation of small portion of chromosomes