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Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz
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 diagr...
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| Autoren: | , , |
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| Formato: | Artigo |
| Idioma: | inglês |
| Publicado em: |
Philipps-Universität Marburg
2024
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| Assuntos: | |
| Acesso em linha: | Texto integral em PDF |
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| Resumo: | 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. |
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| Descrição do item: | Gefördert durch den Open-Access-Publikationsfonds der UB Marburg. |
| DOI: | 10.1038/s41598-023-49179-x |