Cytoscape.js statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Cytoscape.js

Tool usage distribution map

This map represents all the scientific publications referring to Cytoscape.js per scientific context
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Cytoscape.js specifications


Unique identifier OMICS_10135
Name Cytoscape.js
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Gary Bader

Publication for Cytoscape.js

Cytoscape.js citations


IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics

Sci Rep
PMCID: 5847565
PMID: 29531263
DOI: 10.1038/s41598-018-22631-z

[…] e result of user queries for these associations in two ways: (a) A table of associations with references to literature sources, and (b) A network visualization of the associations which is powered by Cytoscape.js (Fig. ). In addition, users can also download the result of their queries for different associations of medicinal plants as a tab-separated list using the available export option in the w […]


iPTMnet: an integrated resource for protein post translational modification network discovery

Nucleic Acids Res
PMCID: 5753337
PMID: 29145615
DOI: 10.1093/nar/gkx1104
call_split See protocol

[…] erlying system components to support interactive scientific queries and visualization of PTM data. The website provides two types of visualization: the Cytoscape () network view, implemented with the Cytoscape.js (version 2.4.2) graph theory library, and the multiple sequence alignment view. Multiple sequence alignments are performed using MUSCLE (). […]


NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium scale biological networks

BMC Res Notes
PMCID: 5513407
PMID: 28705239
DOI: 10.1186/s13104-017-2607-8

[…] e of igraph-R library [] and plots are generated through R and plotly []. Static network visualizations are offered by the d3 library whereas dynamic network visualization is provided by CytoscapeWeb/Cytoscape.js [, ]. […]


Contextualization of drug mediator relations using evidence networks

BMC Bioinformatics
PMCID: 5471944
PMID: 28617226
DOI: 10.1186/s12859-017-1642-8

[…] the interpretability of the EDDY-CTRP results by generating evidence networks of the most relevant intermediate genes using the STRING and STITCH knowledge-bases. With these evidence networks and our Cytoscape.js-based user interface, we expect that the EDDY-CTRP results can be used to form hypotheses based on these contextualized drug-mediator pairs.Besides facilitating drug-mediator pair interpr […]


CorNet: Assigning function to networks of co evolving residues by automated literature mining

PLoS One
PMCID: 5436653
PMID: 28545124
DOI: 10.1371/journal.pone.0176427
call_split See protocol

[…] The CMA network visualization tool was built using cytoscape.js (a JavaScript graph visualization library)[] and jquery (user interface libraries). In this HTML based network viewer nodes represent alignment positions (with the MSA position number ind […]


SBSPKSv2: structure based sequence analysis of polyketide synthases and non ribosomal peptide synthetases

Nucleic Acids Res
PMCID: 5570206
PMID: 28460065
DOI: 10.1093/nar/gkx344
call_split See protocol

[…] enzymes involved in the characterized PKs/NRPs pathway have been stored. The PK and NRP pathways have been represented as interactive graphs (Figure ). The pathway pages use embedded JavaScript-based Cytoscape.js (). Each graph starts with the starter moiety and catalogs the intermediate steps to terminate at the complete metabolite. The nodes of the graph represent the biosynthetic intermediates […]

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Cytoscape.js institution(s)
The Donnelly Centre, University of Toronto, Toronto, ON, Canada
Cytoscape.js funding source(s)
NRNB (U.S. National Institutes of Health, National Center for Research Resources grant P41 GM103504); NIH grants R01GM070743 and U41HG006623

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