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Juicebox specifications

Information


Unique identifier OMICS_13560
Name Juicebox
Alternative names juicebox.js, hic-viz
Software type Package/Module
Interface Web user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Javascript
Parallelization CUDA
License MIT License
Computer skills Basic
Version 1.0.2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Aiden E.L. <>

Additional information


https://igvteam.github.io/juicebox.js/

Publications for Juicebox

Juicebox in publications

 (19)
PMCID: 5899154
PMID: 29654311
DOI: 10.1038/s41467-018-03614-0

[…] architecture., hi-c interaction matrices for k562 (female), hmec (male), nhek (unisex), sperm (male), patski fibroblasts (female), and mouse neuronal stem cells (male) were downloaded using the juicebox software,,, and the heatmaps were generated with the publicly available script “heatmap.pl” available through github (https://github.com/dekkerlab/cworld-dekker). the rpe-1 (female) and mesc […]

PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] observed interactions between them. plotting contact probabilities versus genomic distance typically reveals an inverse relationship between these two parameters. hi-c data can be visualized using juicebox [], my5c [] and 3d genome browsers [] and higlass []. epigenome browser combines web technology with intuitive graphical design to visualize long-range interaction data [,]. beside chromatin […]

PMCID: 5773513
PMID: 29348612
DOI: 10.1038/s41467-017-02596-9

[…] their accompanying genotype data derived from low-pass whole-genome sequencing as a part of 1000 genomes project. snp regions were also assessed with hi-seq and chia-pet chromosomal structure using juicebox and data from lymphoblastoid cell lines only. online databases, namely regulomedb and haploreg, were utilized to glean functional information on snps., this study used biospecimens […]

PMCID: 5647326
PMID: 29044103
DOI: 10.1038/s41467-017-01122-1

[…] to genes within the same tad, the enrichment of particular transcription factors in the same tad suggests that they co-regulate genes found in the tad. to visually demonstrate our analysis, we used “juicebox” software for visualizing data from hi-c mapping experiments. by this analysis, for example, the mitf target gene trpm1 was found to be in an oct4 and mitf shared tad (fig. ), supporting […]

PMCID: 5607496
PMID: 28931413
DOI: 10.1186/s13059-017-1310-3

[…] reported in situ hi-c data [] is publicly available through sequencing read archive (sra) bioproject number prjna385337. processed hi-c data are available through the visualization software tool juicebox (http://www.aidenlab.org/juicebox/). tf footprinting scripts were obtained from https://bitbucket.org/thashim/piq-single (piq r scripts pwmmatch.exact.r, pairedbam2rdata.r, pertf.bg.r […]


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Juicebox institution(s)
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA; Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA; Department of Computer Science, University of California, Berkeley, CA, USA; Erik Jonsson School of Engineering and Computer Science, University of Texas at Dallas, Richardson, TX, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Computational and Systems Biology, MIT, Cambridge, MA, USA; DMU College of Osteopathic Medicine, Des Moines University, Des Moines, IA, USA; Houston Zoo, Houston, TX, USA; Wildlife Conservation Society, New York, NY, USA; Revive and Restore, Sausalito, CA, USA
Juicebox funding source(s)
Supported by a Center for Theoretical Biological Physics postdoctoral fellowship, an NIH New Innovator Award (1DP2OD008540-01), an NSF Physics Frontiers Center Award (PHY-1427654, Center for Theoretical Biological Physics), the Welch Foundation (Q-1866), an NVIDIA Research Center Award, an IBM University Challenge Award, a Google Research Award, a Cancer Prevention Research Institute of Texas Scholar Award (R1304), a McNair Medical Institute Scholar Award, an NIH 4D Nucleome Grant U01HL130010, an NIH Encyclopedia of DNA Elements (ENCODE) Mapping Center Award UM1HG009375, the President’s Early Career Award in Science and Engineering.

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