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| Item Type: | Article |
|---|---|
| Title: | Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz |
| Creators Name: | Race, A.M. and Fuchs, A. and Chung, H.R. |
| Abstract: | Chromosome conformation capture (3C) sequencing approaches, like Hi-C or micro-C, allow for an unbiased view of chromatin interactions. Most analysis methods rely on so-called interaction matrices, which are derived from counting read pairs in bins of fixed size. Here, we propose the Voronoi diagram, as implemented in Voronoi for chromosome conformation capture data visualization (v3c-viz) to visualize 3C data. The Voronoi diagram corresponds to an adaptive-binning strategy that adapts to the local densities of points. In this way, visualization of data obtained by moderate sequencing depth pinpoint many, if not most, interesting features such as high frequency contacts. The favorable visualization properties of the Voronoi diagram indicate that the Voronoi diagram as density estimator can be used to identify high frequency contacts at a resolution approaching the typical size of enhancers and promoters. v3c-viz is available at https://github.com/imbbLab/v3c-viz . |
| Keywords: | Chromatin, Chromosomes, Genetic Promoter Regions, Molecular Conformation, Nucleic Acid Regulatory Sequences |
| Source: | Scientific Reports |
| ISSN: | 2045-2322 |
| Publisher: | Nature Publishing Group |
| Volume: | 13 |
| Number: | 1 |
| Page Range: | 22020 |
| Date: | 12 December 2023 |
| Official Publication: | https://doi.org/10.1038/s41598-023-49179-x |
| PubMed: | View item in PubMed |
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