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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

Versioning


No version available

Maintainer


  • person_outline Bianca H. Habermann

Publication for KEGGViewer

KEGGViewer citations

 (5)
library_books

Practical aspects of NGS based pathways analysis for personalized cancer science and medicine

2016
Oncotarget
PMCID: 5239569
PMID: 27191992
DOI: 10.18632/oncotarget.9370

[…] k can 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, faci […]

library_books

Tools for visualization and analysis of molecular networks, pathways, and omics data

2015
PMCID: 4461095
PMID: 26082651
DOI: 10.2147/AABC.S63534

[…] knowledge of JSON (JavaScript Object Notation) and JavaScript. While the learning curves for the latter programs are steeper, both tools offer useful functionalities, such as looping over conditions (KEGGViewer) or mapping several conditions on the same pathway map (PathVisio).In general, each pathway visualization tool has advantages and disadvantages. While we give examples only for a very small […]

call_split

Dissecting microbial community structure and methane producing pathways of a full scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing

2015
Microb Cell Fact
PMCID: 4381419
PMID: 25880314
DOI: 10.1186/s12934-015-0218-4
call_split See protocol

[…] . 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 A (FmdA […]

call_split

Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

2014
PLoS One
PMCID: 4031174
PMID: 24852573
DOI: 10.1371/journal.pone.0098425
call_split See protocol

[…] 0−2 . 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 con […]

library_books

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

2011
BMC Bioinformatics
PMCID: 3044276
PMID: 21342551
DOI: 10.1186/1471-2105-12-S1-S21

[…] MEGAN includes a module called ‘KEGGviewer’ for the analysis of metagenomic data in the context of pathways. It is designed to consume a list of RefSeq accession numbers and maps them to KEGG orthologies (KO numbers). The functional […]

Citations

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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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