KEGGViewer protocols

View KEGGViewer computational protocol

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KEGGViewer specifications

Information


Unique identifier OMICS_08976
Name KEGGViewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bianca H. Habermann <>

Publication for KEGGViewer

KEGGViewer in pipeline

2015
PMCID: 4381419
PMID: 25880314
DOI: 10.1186/s12934-015-0218-4

[…] detailed analysis of the anaerobic digestion sludge was conducted to count and compare the hit numbers of the sequences of corresponding enzymes subunits in the methanogenesis pathways. the module ‘keggviewer’ in megan was used to analyze pathways [,]. proteins glutathione-independent formaldehyde dehydrogenase (fdha), hydrogenase subunit a(echa), formylmethanofuran dehydrogenase subunit […]


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KEGGViewer in publications

 (5)
PMCID: 5239569
PMID: 27191992
DOI: 10.18632/oncotarget.9370

[…] be browsed with google maps interface allowing various zoom levels., several pathway resources provide a web interface allowing to overlay researcher's own data on available pathways. for example keggviewer [] and reactome [] provide tools for coloring pathways according to expression data. acsn resource allows users to overlay any expression, copy-number and mutation data on cancer maps, […]

PMCID: 4461095
PMID: 26082651
DOI: 10.2147/AABC.S63534

[…] a set of user-provided genes. pathway projector was, for instance, used to visualize metabolic changes upon nitrogen deficiency of the oil-rich algae pseudochoricystis ellipsoidea., finally, with keggviewer, users can integrate expression data with kegg pathways and create a web-based visualization using the open-source javascript library biojs. keggviewer is purely web based. visualization […]

PMCID: 4381419
PMID: 25880314
DOI: 10.1186/s12934-015-0218-4

[…] detailed analysis of the anaerobic digestion sludge was conducted to count and compare the hit numbers of the sequences of corresponding enzymes subunits in the methanogenesis pathways. the module ‘keggviewer’ in megan was used to analyze pathways [,]. proteins glutathione-independent formaldehyde dehydrogenase (fdha), hydrogenase subunit a(echa), formylmethanofuran dehydrogenase subunit […]

PMCID: 4031174
PMID: 24852573
DOI: 10.1371/journal.pone.0098425

[…] . the resulting blastp files were analyzed according to ncbi taxonomy using megan software version 4.70.4 with the following lca parameters: min score, 50; top percent, 10.0; min support, 5 . the keggviewer module in megan was used to map the sequences in each sample to kegg pathways . program pems, which is based on tetranucleotide blsom was used for the taxonomic assignment of metagenome […]

PMCID: 3044276
PMID: 21342551
DOI: 10.1186/1471-2105-12-S1-S21

[…] of eight bergen marine samples based on their functional content using goodall’s index. finally it is also possible to compare pathways present in multiple microbial communities using megan’s keggviewer. one can compare multiple datasets using different colors see figure ., a first comparison between megan and mg-rast was performed with a small subset of an flx-titanium pyrosequencing […]


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KEGGViewer institution(s)
Max Planck Institute of Biochemistry, Germany; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
KEGGViewer funding source(s)
This work was supported by the Max Planck Society.

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