ArticleBioinformatics (Oxford, England)2020
HiChIP-Peaks: a HiChIP peak calling algorithm.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A novel super-enhancer-driven lncRNA LINC00973 governs head and neck squamous cell carcinoma progression through EN2.Cell death & disease · 2025Article
- Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide CRISPR screen identifies IRF1 and TFAP4 as transcriptional regulators of Galectin-9 in T cell acute lymphoblastic leukemia.Science advances · 2025Article
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- CD-Loop: a chromatin loop detection method based on the diffusion model.Frontiers in genetics · 2024Article
- Regulation of CTCF loop formation during pancreatic cell differentiation.Nature communications · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- 3D chromatin architecture and transcription regulation in cancer.Journal of hematology & oncology · 2022Review
- STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming.Nature communications · 2022Article
- cLoops2: a full-stack comprehensive analytical tool for chromatin interactions.Nucleic acids research · 2022Article
- High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma.Frontiers in cell and developmental biology · 2022Article
- Disruption of c-MYC Binding and Chromosomal Looping Involving Genetic Variants Associated With Ankylosing Spondylitis Upstream of theFrontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationHiChIP is a powerful tool to interrogate 3D chromatin organization. Current tools to analyse chromatin looping mechanisms using HiChIP data require the identification of loop anchors to work properly. However, current approaches to discover these anchors from HiChIP data are not satisfactory, having either a very high false discovery rate or strong dependence on sequencing depth. Moreover, these tools do not allow quantitative comparison of peaks across different samples, failing to fully exploit the information available from HiChIP datasets.
resultsWe develop a new tool based on a representation of HiChIP data centred on the re-ligation sites to identify peaks from HiChIP datasets, which can subsequently be used in other tools for loop discovery. This increases the reliability of these tools and improves recall rate as sequencing depth is reduced. We also provide a method to count reads mapping to peaks across samples, which can be used for differential peak analysis using HiChIP data. AVAILABILITY AND IMPLEMENTATION: HiChIP-Peaks is freely available at https://github.com/ChenfuShi/HiChIP_peaks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.