Cytoscape protocols

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Cytoscape computational protocol

Cytoscape specifications

Information


Unique identifier OMICS_04119
Name Cytoscape
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.6.1
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Cytoscape

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Maintainer


  • person_outline Trey Ideker <>

Publication for Cytoscape

Cytoscape IN pipelines

 (220)
2018
PMCID: 5774689
PMID: 29351308
DOI: 10.1371/journal.pone.0190933

[…] assess the uncertainty in the hierarchical clustering analysis on 10,000 bootstrap replicates [22]., functional annotations and pathway analyses of degs were carried out using the cluego plug-in of cytoscape [23]. gene ontology (go) annotates genes to biological/cellular/molecular terms in a hierarchically structured manner, whereas the kyoto encyclopedia of genes and genomes (kegg) [24] […]

2018
PMCID: 5784662
PMID: 29368590
DOI: 10.1186/s12870-017-1220-2

[…] plit = 2) to cluster splitting [22]. the resulting genes (threshold weight ≥ 0.1) involved in psarfs was analyzed with bgi wego (http://wego.genomics.org.cn/) to assign gene ontology (go) terms [54]. cytoscape was implemented for visualizing interaction networks [39]., the recent development of the rna-seq method provides information on wide and sensitive gene expression. in our rna-seq data, the […]

2018
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] was used to normalize the background read count of the genes belonging to each cluster., the gene ontology terms enriched in each cluster of genes were obtained with the plugin bingo [164] in cytoscape v3.1.1 [165] with default parameters. the ontology terms and corresponding d. melanogaster annotations were downloaded from geneontology.org [166,167] (as of january 2015)., […]

2018
PMCID: 5799454
PMID: 29402919
DOI: 10.1038/s41598-018-20679-5

[…] co-expression network was constructed via wgnca r package58. network nodes represent gene expression profiles, while undirected edges values are the pairwise correlations between gene expressions. cytoscape software (http://www.cytoscape.org/) was used for network import and visualization., using human gene sequences available from ncbi (www.ncbi.nlm.nih.gov/nucleotide), pcr oligonucleotide […]

2018
PMCID: 5799454
PMID: 29402919
DOI: 10.1038/s41598-018-20679-5

[…] via wgnca r package58. network nodes represent gene expression profiles, while undirected edges values are the pairwise correlations between gene expressions. cytoscape software (http://www.cytoscape.org/) was used for network import and visualization., using human gene sequences available from ncbi (www.ncbi.nlm.nih.gov/nucleotide), pcr oligonucleotide for sense genes pairs […]

Cytoscape institution(s)
Institute for Systems Biology, Seattle, WA, USA

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