3D Genome Browser statistics

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3D Genome Browser specifications

Information


Unique identifier OMICS_15678
Name 3D Genome Browser
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Feng Yue <>

Publication for 3D Genome Browser

3D Genome Browser in publications

 (7)
PMCID: 5847529
PMID: 29531215
DOI: 10.1038/s41467-018-03411-9

[…] for a non-coding rna, this non-coding rna is listed along with the nearest protein-coding gene (table¬†)., in order to align chi-c data with tads, we accessed hi-c data generated in hmecs through the 3d genome browser (http://promoter.bx.psu.edu/)., tcga breast cancer (brca) data set was used to test for an association between genotype and mrna abundance further adjusted for dna methylation […]

PMCID: 5821732
PMID: 29467363
DOI: 10.1038/s41467-018-03113-2

[…] in the github repository (https://github.com/zhangyan32/hicplus). enhanced hi-c datasets can be downloaded from http://promoter.bx.psu.edu/public/hicplus/matrix/ and can be visualized in the 3d genome browser (http://3dgenome.org)., , yan zhang¬†and lin an contributed equally to this work., electronic supplementary material , supplementary information accompanies this paper […]

PMCID: 5703900
PMID: 29180618
DOI: 10.1038/s41467-017-01804-w

[…] lncrna: same as above, but with any part of the transcript was marked as typical enhancer. (4) unmarked lncrna if no chromatin marked was present on the gene., hi-c plots were generated using the 3d genome browser (http://promoter.bx.psu.edu/hi-c/index.html) using publicly available hi-c data on mouse escs., grna design and production of crispr-cas9 nickase constructs: guide rnas (grnas) […]

PMCID: 5739635
PMID: 29285248
DOI: 10.18632/oncotarget.22165

[…] was analyzed with gfold []., hi-c data of a549 was obtained from encode3, generated by dekker laboratory (encff478eab, encff319ast, encff805bpj and encff582xkw). the heat map was generated by 3d genome browser (http://www.3dgenome.org.)., we surgically harvested 71 lung adenocarcinoma samples and paired adjacent normal tissue samples (>2 cm away from the tumor) from patients […]

PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y

[…] data. here, we investigate five tools that can be operated using a web browser or a graphical user interface: hi-browse v1.6 [], my5c [], juicebox v1.5 [], the epigenome browser v40.6 [] and the 3d genome browser [] (table ). these tools do not require programming expertise, and are more readily accessible. we assess these tools using several criteria, such as the types of visualizations […]


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3D Genome Browser institution(s)
College of Medicine, Biochemistry and Molecular Biology, The Pennsylvania State University, Hershey, PA, USA

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