ArticleNature communications2021
HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- LAWS-HiC: A Locally Adaptive Weighting and Screening (LAWS) Approach to Improve Detection of Long-Range Chromatin Interactions from Hi-C Data.Methods and protocols · 2026Article
- HiCPotts: an R/bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias.Bioinformatics (Oxford, England) · 2026Article
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Assessing reproducibility of Hi-C chromatin interactions using stratum-adjusted irreproducible discovery rate.Bioinformatics (Oxford, England) · 2026Article
- HiC2Self: Self-supervised denoising for bulk and single-cell Hi-C contact maps.Science advances · 2026Article
- Initial leukemic epigenomic state determines hypomethylating agent response.Nature communications · 2026Article
- UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility.Nucleic acids research · 2026Article
- Functional chromatin signatures premark future lineage-specific enhancers.Cell genomics · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- FourC: identifying significant and differential contacts in 1D chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- EpiExpr: Predicting gene expression using epigenetic data and chromatin interactions.bioRxiv : the preprint server for biology · 2026Article
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.Communications biology · 2026Article
- DiffHiChIP: Identifying differential chromatin contacts from HiChIP data.Cell reports methods · 2025Article
- PB-DiffHiC: a statistical framework for detecting differential chromatin interactions from high resolution pseudo-bulk Hi-C data.BMC genomics · 2025Article
- Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T-cell differentiation.Protein & cell · 2025Article
- Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.iScience · 2025Article
- Disruption of TAD hierarchy promotes LTR co-option in cancer.Nature genetics · 2025Article
- Recipes and ingredients for deep learning models of 3D genome folding.Current opinion in genetics & development · 2025Review
- A comprehensive review and benchmark of differential analysis tools for Hi-C data.Briefings in bioinformatics · 2025Review
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6 authors.
Funding
Abstract
Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool for Hi-C/HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools and includes topologically associating domain (TAD) and A/B compartment callers. We found that HiC-DC+ can more accurately identify enhancer-promoter interactions in H3K27ac HiChIP, as validated by CRISPRi-FlowFISH experiments, compared to existing methods. Differential HiC-DC+ analyses of published HiChIP and Hi-C data sets in settings of cellular differentiation and cohesin perturbation systematically and quantitatively recovers biological findings, including enhancer hubs, TAD aggregation, and the relationship between promoter-enhancer loop dynamics and gene expression changes. HiC-DC+ therefore provides a principled statistical analysis tool to empower genome-wide studies of 3D chromatin architecture and function.
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