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Protocols

RBGL specifications

Information


Unique identifier OMICS_16859
Name RBGL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Artistic License version 2.0
Computer skills Advanced
Version 1.56.0
Stability Stable
Requirements
methods, BiocGenerics, RUnit, graph, Rgraphviz, XML
Maintained Yes

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  • person_outline Vince Carey

RBGL citations

 (8)
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Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response

2017
BMC Plant Biol
PMCID: 5540570
PMID: 28764653
DOI: 10.1186/s12870-017-1077-4
call_split See protocol

[…] The R package of RBGL v 1.44.0 (http://bioconductor.org/packages/RBGL/) is used to calculate the clustering coefficient of the maize GGM network. The network was clustered via the MCL clustering algorithm, using these […]

library_books

TopoICSim: a new semantic similarity measure based on gene ontology

2016
BMC Bioinformatics
PMCID: 4966780
PMID: 27473391
DOI: 10.1186/s12859-016-1160-0

[…] used to weigh the GO terms were calculated using the GOSim package (version 1.8.0) []. For each disjunctive the shortest path between the two GO terms was calculated by the Dijkstra algorithm in the RBGL package (version 1.46.0) [] according to (). Also the longest path between the disjunctive and root was calculated by the topology sorting algorithm [] according to (). […]

library_books

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin

2016
BMC Genomics
PMCID: 4888481
PMID: 27245696
DOI: 10.1186/s12864-016-2718-y

[…] ed if both interaction partners were within the set of remaining seeds. The corresponding networks were then visualized using Cytoscape [] and topological properties were calculated using the igraph, RBGL, and QuACN packages in R [–]. The information-theoretic distance measure was calculated by the infoTheoreticGCM method (parameter: coeff=”exp”) as provided by the QuACN package []. For analyzing […]

library_books

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

2015
F1000Res
PMCID: 4670004
PMID: 26672762
DOI: 10.5256/f1000research.7270.r9848

[…] the Bioconductor group to produce the RCy3 harmonization library for R , which leverages cyREST to realize native R network visualization, analysis, and publishing functions. Its igraph, graph , and RBGL packages are useful components for network data analysis workflows. […]

library_books

Visualizing collaborative electronic health record usage for hospitalized patients with heart failure

2015
PMCID: 4394967
PMID: 25710558
DOI: 10.1093/jamia/ocu017

[…] on a more global level. Clique membership and size within the provider collaboration network were identified using the kCliques algorithm, which is part of the Boost Graph Library interface package (RBGL) for the R statistical computing environment. Figure 4:: […]

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Graphical Modeling of Gene Expression in Monocytes Suggests Molecular Mechanisms Explaining Increased Atherosclerosis in Smokers

2013
PLoS One
PMCID: 3553098
PMID: 23372645
DOI: 10.1371/journal.pone.0050888
call_split See protocol

[…] rresponding to covariates. Whenever more than one shortest path existed, the algorithm chooses one according to a greedy search. The Dijkstra's algorithm implemented in the sp.between function of the RBGL package for R was used .Note that although in its full version the PC algorithm (Algorithm 2 in ) can asymptotically infer causal associations in a network by directing some of the edges of the s […]


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