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DyNet specifications

Information


Unique identifier OMICS_11674
Name DyNet
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 0.9.1
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Maintainer


  • person_outline David J. Lynn <>

Publication for DyNet

DyNet in pipeline

2017
PMCID: 5805521
PMID: 29467935
DOI: 10.18632/oncotarget.23490

[…] ≤ 0.001). gene co-expression networks were generated for normal lung gene expression data (gtex) and lung adenocarcinoma (tcga) and visualized using cytoscape 3.4.0. (http://www.cytoscape.org). dynet was used to highlight differences between two networks based on node and edge presence, cluego was used to identify significantly enriched biological pathways [, ]., 100 random selections […]


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DyNet in publications

 (4)
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] obtained from all bootstrap networks previously generated. early and late consensus networks were imported into cytoscape 3.4 (http://www.cytoscape.org/cy3.html) and they were compared with the dynet algorithm [] in order to identify the most rewired nodes, by ranking the nodes with a decreasing dn score. to select a robust target core subnetwork of itreg signature genes in the vicinity […]

PMCID: 5805521
PMID: 29467935
DOI: 10.18632/oncotarget.23490

[…] ≤ 0.001). gene co-expression networks were generated for normal lung gene expression data (gtex) and lung adenocarcinoma (tcga) and visualized using cytoscape 3.4.0. (http://www.cytoscape.org). dynet was used to highlight differences between two networks based on node and edge presence, cluego was used to identify significantly enriched biological pathways [, ]., 100 random selections […]

PMCID: 5686481
PMID: 29188012
DOI: 10.5256/f1000research.9906.r17046

[…] is achieved by comparing the networks under investigation, with some randomly generated networks., it is important to note that some apps that allow performing network comparison exist. for instance dynet , gasoline , netmatch* , and randomnetworks . randomnetworks has a lot of similarities with our app but is no longer maintained and it works only with cytoscape 2.x which makes it useless […]

PMCID: 5406835
PMID: 28447619
DOI: 10.1038/srep46239

[…] changes. the reactome analysis of proteins was performed using the string algorithm. overlay analysis of the two resulting reactome networks was prepared in the software cytoscape v3.4.0 using the dynet application., the samples were eluted from cambridge filters in 5 ml of methanol. the filters were placed in glass vials, methanol was added, and they were vortexed for 1 minute, followed […]


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DyNet institution(s)
EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Medical and Health Research Institute, North Terrace, Adelaide, SA, Australia; School of Medicine, Flinders University, Bedford Park, SA, Australia
DyNet funding source(s)
The European Union Seventh Framework Programme (FP7/2007-2013) PRIMES project under grant agreement number FP7-HEALTH-2011-278568; EMBL Australia

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