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Abstract SummaryHiCube is a lightweight web application for interactive visualization and exploration of diverse types of genomics data at multiscale resolutions. Especially, HiCube displays synchronized views of Hi-C contact maps and 3D genome structures with user-friendly annotation and configuration tools, thereby facilitating the study of 3D genome organization and function. Availability and implementationHiCube is implemented in Javascript and can be installed via NPM. The source code is freely available at GitHub (https://github.com/wmalab/HiCube).
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HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting
Abstract MotivationThe exploration of the 3D organization of DNA within the nucleus in relation to various stages of cellular development has led to experiments generating spatiotemporal Hi-C data. However, there is limited spatiotemporal Hi-C data for many organisms, impeding the study of 3D genome dynamics. To overcome this limitation and advance our understanding of genome organization, it is crucial to develop methods for forecasting Hi-C data at future time points from existing timeseries Hi-C data. ResultIn this work, we designed a novel framework named HiCForecast, adopting a dynamic voxel flow algorithm to forecast future spatiotemporal Hi-C data. We evaluated how well our method generalizes forecasting data across different species and systems, ensuring performance in homogeneous, heterogeneous, and general contexts. Using both computational and biological evaluation metrics, our results show that HiCForecast outperforms the current state-of-the-art algorithm, emerging as an efficient and powerful tool for forecasting future spatiotemporal Hi-C datasets. Availability and implementationHiCForecast is publicly available at https://github.com/OluwadareLab/HiCForecast.
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- Award ID(s):
- 2153205
- PAR ID:
- 10570096
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- Volume:
- 41
- Issue:
- 2
- ISSN:
- 1367-4811
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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