Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data
Year: 2018
Type: article
Abstract: Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.
Source: Cell Systems
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $9,350
Funders: National Science Foundation, Welch Foundation, Cancer Prevention and Research Institute of Texas, Google, Nvidia, Instituto Tecnológico de Costa Rica, National Institutes of Health, National Heart, Lung, and Blood Institute, National Human Genome Research Institute, National Cancer Institute, National Institute of General Medical Sciences
Awards: G1047773206, A next-generation Integrative Genomics Viewer for biomedical and cancer research., The Integrative Genomics Viewer (IGV): visualization supporting cancer research, Beyond pairwise DNA contacts: exploring higher-order genome structure using proximity ligation, G2837517328, G4026285588, GENOME WIDE MAPPING OF LOOPS USING IN SITU HI-C, G508817667, G5224893814, Exploring how the genome folds through proximity ligation and sequencing, Center for Theoretical Biological Physics - Houston, Recruitment of First-Time, Tenure-Track Faculty Members, Supporting Integrative Genomic Analysis Users with GenePattern
OpenAlex ID: W2765865112