ArticleBioinformatics (Oxford, England)2019
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- High-resolution promoter interaction analysis implicates genes involved in activation of type 3 innate lymphoid cells in immune disease risk.Nature genetics · 2026Article
- An EGR1-dependent cascade modulates genome architecture at the CSF1R locus.Nucleic acids research · 2026Article
- High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk.bioRxiv : the preprint server for biology · 2026Article
- DiffHiChIP: Identifying differential chromatin contacts from HiChIP data.Cell reports methods · 2025Article
- Integrated promoter-capture Hi-C and Hi-C analysis reveals fine-tuned regulation of the 3D chromatin architecture in colorectal cancer.Frontiers in genetics · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Increased enhancer-promoter interactions during developmental enhancer activation in mammals.Nature genetics · 2024Article
- The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.Nature structural & molecular biology · 2024Article
- Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions.BMC biology · 2023Article
- Functional characterization of Alzheimer's disease genetic variants in microglia.Nature genetics · 2023Article
- Identification of Mechanisms by Which Genetic Susceptibility Loci Influence Systemic Sclerosis Risk Using Functional Genomics in Primary T Cells and Monocytes.Arthritis & rheumatology (Hoboken, N.J.) · 2023Article
- Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin.Epigenetics & chromatin · 2022Article
- Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Nature protocols · 2021Article
- 3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders.Progress in neurobiology · 2021Article
- 3D reconstruction of genomic regions from sparse interaction data.NAR genomics and bioinformatics · 2021Article
- Assessment of 3D Interactions Between Promoters and Distal Regulatory Elements with Promoter Capture Hi-C (PCHi-C).Methods in molecular biology (Clifton, N.J.) · 2021Article
- HCMB: A stable and efficient algorithm for processing the normalization of highly sparse Hi-C contact data.Computational and structural biotechnology journal · 2021Article
- Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers.Cell reports · 2020Article
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4 authors.
Funding
Abstract
summaryCapture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package for robust detection of differential interactions in Capture Hi-C data. Chicdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalization and multiple testing procedures that account for specific statistical properties of Capture Hi-C. We validate Chicdiff on published Promoter Capture Hi-C data in human Monocytes and CD4+ T cells, identifying multitudes of cell type-specific interactions, and confirming the overall positive association between promoter interactions and gene expression. AVAILABILITY AND IMPLEMENTATION: Chicdiff is implemented as an R package that is publicly available at https://github.com/RegulatoryGenomicsGroup/chicdiff. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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