Source code for the paper S. Fujishiro and M. Sasai "Generation of dynamic three-dimensional genome structure through phase separation of chromatin" (2022). The project covers:

• Novel annotation of local chromatin using NCI, or the diagonal signal of Hi-C contact matrix
• 1kb-resolution chromatin dynamics simulations
• 100kb-resolution whole-genome interphase chromatin dynamics simulations
• 10Mb-resolution whole-genome ana/telophase chromatin dynamics simulations
• Coarse-graining of chromatin polymer based on the PRISM-theory

• Directories
• License

• 1-hic: Preparation of chromosome contact maps. Downloads and preprocesses Hi-C dataset.
• 2-signal: Analysis of the contact maps. Computes compartment signal and NCI.
• 3-sim-1kb: Chromatin dynamics at 1kb resolution. Incorporates kinetic HP-1 attraction and cohesin looping. Estimates effective interaction among 100kb chromatin regions using PRISM theory.
• 4-sim-ab: Simulation of phase separation in purely repulsive polymer blend.
• 5-sim-genome: Simulation of human genome in ana/telophase and interphase.

MIT License