ArticleBMC bioinformatics2015
HiCdat: a fast and easy-to-use Hi-C data analysis tool.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- BMI1s interact with condensin complexes to regulate chromatin 3D structure and gene expression inaBIOTECH · 2025Article
- Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation.NAR genomics and bioinformatics · 2025Article
- The 3D genome of plasma cells in multiple myeloma.Scientific reports · 2025Article
- A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication.Nature structural & molecular biology · 2024Article
- PWOs repress gene transcription by regulating chromatin structures in Arabidopsis.Nucleic acids research · 2024Article
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken.Communications biology · 2024Article
- Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.Nature communications · 2024Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Integrative Identification by Hi-C Revealed Distinct Advanced Structural Variations in Lung Adenocarcinoma Tissue.Phenomics (Cham, Switzerland) · 2023Article
- Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins.Nature plants · 2022Article
- Chromatin remodeling complexes regulate genome architecture in Arabidopsis.The Plant cell · 2022Article
- 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing.Acta pharmaceutica Sinica. B · 2021Article
- FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.Genome biology · 2020Article
- Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.BMC bioinformatics · 2020Article
- The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.BMC bioinformatics · 2020Article
- Enhancer variants associated with Alzheimer's disease affect gene expression via chromatin looping.BMC medical genomics · 2019Article
- Review
- Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana.Genome biology · 2019Article
- Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution.Nature communications · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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Abstract
backgroundThe study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.
resultsHiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).
conclusionsHiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.
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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.