Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Networks02:26

Protein Networks

4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
Protein Networks02:26

Protein Networks

2.7K
2.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Integration of human and mouse single-cell transcriptomes of the developing cerebellum nominates cells-of-origin for group 3 and 4 medulloblastoma.

BMC cancer·2026
Same author

Genetic regulators of neuronal survival across metabolic environments.

bioRxiv : the preprint server for biology·2026
Same author

Tutorial: annotation of animal genomes.

Nature protocols·2026
Same author

Epigenomic landscape of the developing human rhombic lip reveals gene regulatory network and non-coding loci of developmental, evolutionary, and disease relevance.

bioRxiv : the preprint server for biology·2025
Same author

Fibrin drives thromboinflammation and neuropathology in COVID-19.

Nature·2024
Same author

Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.

Nucleic acids research·2024
Same journal

Sentiment Analysis of Acceptance TVET Online Courses on the Skill Academy App from Google Play: Leveraging Text Mining with Comparison Machine Learning Model.

F1000Research·2026
Same journal

Emotional intelligence: An important skill to learn now more than ever.

F1000Research·2026
Same journal

East Mediterranean Lineage of <i>Brucella melitensis</i> in Human Isolates and Milk Samples in Oman Using MLVA-14.

F1000Research·2026
Same journal

Application of K-Means Clustering for Job Applicant Analysis in Construction Firms Using R.

F1000Research·2026
Same journal

The influence of self-esteem and emotional intelligence on addiction to social networks in Peruvian university students.

F1000Research·2026
Same journal

A Bibliometric Analysis of Music's Role in Promoting Well-Being in Health Science Research.

F1000Research·2026
See all related articles

Related Experiment Video

Updated: Jan 2, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

16.9K

RCy3: Network biology using Cytoscape from within R.

Julia A Gustavsen1, Shraddha Pai2, Ruth Isserlin2

  • 1University of British Columbia, Vancouver, B.C., Canada.

F1000Research
|December 13, 2019
PubMed
Summary
This summary is machine-generated.

RCy3 is a redesigned R package for Cytoscape automation, enhancing network biology workflows. It offers new functions for data overlay and integrates with over 40 Cytoscape apps for broader accessibility.

Keywords:
AutomationBioconductorCytoscapeNetwork biologyScripting

More Related Videos

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.7K
Author Spotlight: Integrating Traditional Chinese Medicine with Modern Pharmacology and Genomics for Assessing Postmenopausal Osteoporosis in Mice
07:20

Author Spotlight: Integrating Traditional Chinese Medicine with Modern Pharmacology and Genomics for Assessing Postmenopausal Osteoporosis in Mice

Published on: August 23, 2024

964

Related Experiment Videos

Last Updated: Jan 2, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

16.9K
Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.7K
Author Spotlight: Integrating Traditional Chinese Medicine with Modern Pharmacology and Genomics for Assessing Postmenopausal Osteoporosis in Mice
07:20

Author Spotlight: Integrating Traditional Chinese Medicine with Modern Pharmacology and Genomics for Assessing Postmenopausal Osteoporosis in Mice

Published on: August 23, 2024

964

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Network Biology

Background:

  • Cytoscape is a widely used platform for network visualization and analysis.
  • Seamless integration between R and Cytoscape is crucial for advanced network biology workflows.
  • Existing tools may lack comprehensive features or ease of use for complex analyses.

Purpose of the Study:

  • To introduce RCy3, a redesigned R package for Cytoscape automation.
  • To enhance the integration of R programming with Cytoscape's full feature set.
  • To streamline the development and usage of network biology workflows.

Main Methods:

  • RCy3 leverages Cytoscape's REST API for seamless communication.
  • The package includes over 100 new functions, with a focus on data overlay.
  • Bi-directional conversion with igraph and graph packages ensures interoperability.

Main Results:

  • Over 40 Cytoscape apps now support automation via RCy3.
  • Hundreds of additional operations are accessible through these integrated apps.
  • Demonstrated use cases include public database integration, enrichment analysis, and shortest path algorithms.

Conclusions:

  • RCy3 significantly enhances network biology research by bridging R and Cytoscape.
  • It enables bioinformaticians to create reproducible and complex network analysis workflows.
  • The package facilitates the integration of Cytoscape functionalities with custom R analyses.