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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

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Publication for RCytoscape

RCytoscape in publications

 (8)
PMCID: 4707277
PMID: 26793190
DOI: 10.3389/fimmu.2015.00644

[…] error-correction scripts were written in python. all remaining analyses were carried out in r, using the following packages: ineq (gini index calculation), vegan (diversity indices), and igraph and rcytoscape (network/cluster analysis). imgt tcr nomenclature and cdr3 definition (running from the last conserved cysteine in the v to the conserved phenylalanine in the fgxg motif in the j gene) […]

PMCID: 4696196
PMID: 26714771
DOI: 10.1186/s12864-015-2351-1

[…] and 249 human proteins. these ppi data sets are provided in the supplementary information (additional file : ppi data)., all networks were plotted in cytoscape [] using r packages igraph and rcytoscape [, ]., we performed two types of gene ontology (go) [] enrichment analysis: standard enrichment analysis and network-based enrichment analysis. both enrichment analyses were performed in r […]

PMCID: 4687084
PMID: 26689934
DOI: 10.1186/s12864-015-2321-7

[…] in r wgcna package (version 1.46) []. correlation threshold was set to 0.9. to obtain edges and nodes, a graphnel-type graph was subsequently generated from the adjacency matrix and sent via the rcytoscape bioconductor package [] to cytoscape application version 2.8.1 [] for cluster visualization and analysis. functions from rcytoscape package were used in order to annotate, select, extend […]

PMCID: 4488272
PMID: 26121354
DOI: 10.1371/journal.pone.0131673

[…] 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., we detail here the results of spearman partial correlation analyses (); standard spearman and pearson, as well as partial pearson, correlations […]

PMCID: 4401789
PMID: 25884760
DOI: 10.1371/journal.pcbi.1004130

[…] 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 […]


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

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