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Protocols

visNetwork specifications

Information


Unique identifier OMICS_16448
Name visNetwork
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Version 2.0.4
Stability Stable
Requirements
methods, stats, utils, grDevices, rmarkdown, knitr, igraph, htmlwidgets, shiny, magrittr, rpart, htmltools, colourpicker, jsonlite, ggraph, R(≥3.0), webshot, shinyWidgets, sparkline, flashClust
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Benoit Thieurmel

visNetwork citations

 (3)
library_books

PIVOT: platform for interactive analysis and visualization of transcriptomics data

2018
BMC Bioinformatics
PMCID: 5756333
PMID: 29304726
DOI: 10.1186/s12859-017-1994-0

[…] Map, PIVOT automatically re-runs analyses and updates parameter choices when needed. Thus, a user can easily compare results of a workflow across derived datasets. The data map is generated with the visNetwork package [] and can be directly edited, so that users can rename nodes, add notes, or delete data subsets and analysis reports that are no longer useful. The full data history is also presen […]

library_books

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria

2017
BMC Genomics
PMCID: 5689173
PMID: 29145803
DOI: 10.1186/s12864-017-4242-0

[…] dependency relationships between phyletic patterns of sRNAs and coding gene elements (5’UTR and CDS) of L. monocytogenes EGD-e. Graph representations were built using the ‘igraph’, version 1.0.1 [], ‘visNetwork’, version 1.0.3 [], and ‘Shiny’, version 1.0.1 [] R packages. […]

call_split

Digging into the low molecular weight peptidome with the OligoNet web server

2017
Sci Rep
PMCID: 5601033
PMID: 28916823
DOI: 10.1038/s41598-017-11786-w
call_split See protocol

[…] first converted to the JSON format and requests to DECOMP are performed using the Rcurl library. The directed PDN is built as an igraph object based on all identified UAAC signals. OligoNet uses the visNetwork package for the network visualization. The KEGGREST library is used for the mass annotation in the KEGG database and for the visualization of metabolic pathways. The client-side interface w […]

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