The Genomic HyperBrowser protocols

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The Genomic HyperBrowser specifications

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Unique identifier OMICS_00638
Name The Genomic HyperBrowser
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Beta
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/The_Genomic_HyperBrowser

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Publications for The Genomic HyperBrowser

The Genomic HyperBrowser in pipelines

 (2)
2016
PMCID: 4939920
PMID: 27029610
DOI: 10.1080/15592294.2016.1169351

[…] states 4–7 as enhancers, 10–11 as transcription, 14–15 as repetitive). the probability of overlap between atrx peaks and the hmm states, genes, promoters and intergenic regions was calculated with the genomic hyperbrowser. atrx peaks were randomized 10,000 times preserving its segment length and inter-segment gaps. observed/expected values were calculated by dividing the overlap of the atrx […]

2014
PMCID: 4304971
PMID: 25338678
DOI: 10.1038/gene.2014.56

[…] density values were calculated using bedtools version 2.1 (). we assessed the statistical significance for the observed enrichments of ch17 snp densities within sds in the ighv and igkv loci using the genomic hyperbrowser (https://hyperbrowser.uio.no()). we created “case-control” tracks including coordinates overlapped (sd) and not overlapped (non-sd) by sds in the ighv/igkv regions, […]


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The Genomic HyperBrowser in publications

 (21)
PMCID: 5591266
PMID: 28887441
DOI: 10.1038/s41467-017-00609-1

[…] with our bioinformatics pipeline to harmonize the integration mapping data. the genomic distribution of integration sites of the different data sets was compared using intervals of 1 mb by the genomic hyperbrowser analysis tool (v2.0b). no significant differences in the global genomic distribution of integration sites were found compared to maldarelli et al., wagner et al., data sets […]

PMCID: 5543110
PMID: 28775312
DOI: 10.1038/s41598-017-07314-5

[…] more than 12,000 human cancers (http://cancer.sanger.ac.uk/cosmic/signatures). plots of normalized mutations frequencies in different trinucleotide sequence contexts were plotted using galaxy and the genomic hyperbrowser., the effect of smug1 and ung knockout on genomic lesion levels were assessed using an unpaired t-test or analysis of variance (anova) on group differences, based on three […]

PMCID: 5144967
PMID: 27694116
DOI: 10.1534/g3.116.033613

[…] to tf name based on id in the jaspar database file. the occurrences of each particular motif were counted within each dmr, and these lists were compared to the list of tfs expressed in germ cells., the genomic hyperbrowser, a web-based platform based on galaxy (https://hyperbrowser.uio.no/hb/), was used to perform statistical analyses comparing the chromosomal distribution of genes […]

PMCID: 4939920
PMID: 27029610
DOI: 10.1080/15592294.2016.1169351

[…] states 4–7 as enhancers, 10–11 as transcription, 14–15 as repetitive). the probability of overlap between atrx peaks and the hmm states, genes, promoters and intergenic regions was calculated with the genomic hyperbrowser. atrx peaks were randomized 10,000 times preserving its segment length and inter-segment gaps. observed/expected values were calculated by dividing the overlap of the atrx […]

PMCID: 4642734
PMID: 26559640
DOI: 10.1186/s13104-015-1624-8

[…] is served as a tool within the galaxy framework, which is an open source, web-based platform for data intensive biomedical research [–]. galaxy is here used in combination with components from the genomic hyperbrowser [, ] as well as google charts for visualization (https://developers.google.com/chart/)., dna variants (single nucleotide variants) can be given either as genomic coordinates […]


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The Genomic HyperBrowser institution(s)
Department of Informatics, University of Oslo, Blindern, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Nydalen, Oslo, Norway; Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway; Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway; Department of Mathematics, University of Oslo, Blindern, Oslo, Norway; Department of Medical Biology, Faculty of Health Science, University of Tromsø, Tromsø, Norway; Statistics For Innovation, Norwegian Computing Center, Oslo, Norway; Bioinformatics Core Facility, Oslo University Hospital and University of Oslo, Nydalen, Oslo, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Informatics, University of Bergen, Bergen, Norway; Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway; Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
The Genomic HyperBrowser funding source(s)
Supported by EMBIO, UiO, Helse Sør-Øst, Norwegian Cancer Society, Elixir-Norway, FUGE and eSysbio (the last two are funded by the Research Council of Norway) and by the Research Council of Norway.

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