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.本仓库包含用于分析与生成人类4D核体（4D Nucleome, 4DN）联盟标志物论文《人类4D核体的结构与功能整合视图》（2025年发表于《自然》（Nature））两个章节的全部核心图表的脚本与输入数据。 三维基因组学检测实验基准评测——评估不同实验平台（Hi-C、Micro-C、CTCF ChIA-PET、RNAPII ChIA-PET及H3K4me3 PLAC-Seq）对各类染色质环的检测性能。 环-转录关联分析——探究环路层面的三维基因组组织与基因转录活性的相关性。 若您使用本仓库中的脚本或数据，请引用以下文献： 4D核体联盟等. 人类4D核体的结构与功能整合视图. 《自然》. 2025.