RCytoscape statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RCytoscape
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Protocols

RCytoscape specifications

Information


Unique identifier OMICS_05213
Name RCytoscape
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for RCytoscape

RCytoscape citations

 (6)
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

[…] hub.com/idekerlab/cy-rest-R License for cyREST, py2cytoscape, and all example workflows: MIT: http://opensource.org/licenses/MIT RCy3 source code: https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape […]

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Tissue Specific Evolution of Protein Coding Genes in Human and Mouse

2015
PLoS One
PMCID: 4488272
PMID: 26121354
DOI: 10.1371/journal.pone.0131673
call_split See protocol

[…] n and 9485 protein-coding genes for mouse were analyzed.All the analysis was performed in R [] using Lattice [] and plyr []. For the representation of the data Cytoscape version 2.8.2 [] with library RCytoscape [] and Circos version 0.62–1 [] were used. […]

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Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts

2015
PLoS Comput Biol
PMCID: 4401789
PMID: 25884760
DOI: 10.1371/journal.pcbi.1004130
call_split See protocol

[…] structure were identified as clusters by the minimum spanning tree, single linkage method []. Three dimensional embeddings of data structure were visualized with PyMOL and Cytoscape, the latter using RCytoscape and three dimensional manipulation functions from the R package, rgl (). Filters were applied to focus on proteins containing tyrosine kinase, tyrosine phosphatase, SH2, and SH3 domains (PN […]

library_books

categoryCompare, an analytical tool based on feature annotations

2014
Front Genet
PMCID: 4010757
PMID: 24808906
DOI: 10.3389/fgene.2014.00098

[…] s available in Bioconductor. The package supports the direct calculation of enriched GO and KEGG annotations on gene lists. Interactive visualization of the annotation graphs is facilitated using the RCytoscape (Shannon, ) Bioconductor package to display the graph in Cytoscape (Shannon et al., ). […]

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R Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

2014
Biology
PMCID: 4009765
PMID: 24833336
DOI: 10.3390/biology3010085
call_split See protocol

[…] opaxParser enable the user to plot pathways via Rgraphviz. Package pathview additionally provides a function to export native KEGG representations as PNG image files. The graphite package, which uses RCytoscape for visualization, as well as RCytoscape itself, visualize graphs via an active Cytoscape session. RCytoscape offers a multitude of well-documented parameters and functions to visualize, la […]

library_books

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways

2013
PLoS One
PMCID: 3536783
PMID: 23300999
DOI: 10.1371/journal.pone.0052884

[…] RCytoscape was used to graph networks and manipulate graphs in Cytoscape. RCytoscape (rcytoscape.systemsbiology.net/versions/current/) is a marriage of Cytoscape , , an open source bioinformatics soft […]


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RCytoscape institution(s)
Fred Hutchison Cancer Research Institute, Seattle, WA, USA

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