4DN Joint Analysis – Chromatin Loop Benchmark and Transcription Association

This repository contains the scripts and input data used to analyze and generate all major figures for two sections of the 4D Nucleome (4DN) Consortium marker paper, “An integrated view of the structure and function of the human 4D nucleome” (Nature, 2025). Benchmarking of 3D genomic assays — evaluating the performance of different experimental platforms (Hi-C, Micro-C, CTCF ChIA-PET, RNAPII ChIA-PET, and H3K4me3 PLAC-Seq) in detecting various classes of chromatin loops. Loop–transcription association analysis — assessing how 3D genome organization at the loop level correlates with gene transcriptional activity. If you use the scripts or data in this repository, please cite: 4D Nucleome Consortium et al. An integrated view of the structure and function of the human 4D nucleome. Nature. 2025.