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Featured Article
https://doi.org/10.12688/f1000research.22280.2
Software Tool Article metrics
Revised
Visualize omics data on networks with Omics Visualizer, a Cytoscape App
[version 2; peer review: 2 approved]
Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
Peer Reviewers Magnus Palmblad; Ruth Isserlin
  • Funders
  • Innovationsfonden
  • Novo Nordisk Fonden
LATEST VERSION PUBLISHED 30 Jun 2020
https://doi.org/10.12688/f1000research.152711.2
Software Tool Article metrics
Revised
Clust&See3.0 : clustering, module exploration and annotation
[version 2; peer review: 2 approved, 1 approved with reservations]
Fabrice Lopez, Lionel Spinelli, Christine Brun
Peer Reviewers Anooja Ali; Ju Xiang; Lun Hu
  • Funder
  • Funding for article processing charges provided by Human Frontier Science Program grant RGP004/2023 to CB.
LATEST VERSION PUBLISHED 14 Nov 2024
https://doi.org/10.12688/f1000research.74395.3
Research Article metrics
Revised
Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces
[version 3; peer review: 2 approved]
Francesco Raimondi, Joshua G. Burkhart, Matthew J. Betts, Robert B. Russell, Guanming Wu
Peer Reviewers Andras Szilagyi; Pier Luigi Martelli
  • Funders
  • Associazione Italiana per la Ricerca sul Cancro
  • Germany Research Foundation
  • Italian Ministry of University and Research
  • Alexander von Humboldt-Stiftung
  • U.S. National Library of Medicine
  • National Human Genome Research Institute
LATEST VERSION PUBLISHED 12 Dec 2022
https://doi.org/10.12688/f1000research.109027.2
Software Tool Article metrics
Revised
Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App
[version 2; peer review: 1 approved, 1 approved with reservations]
Pritam Saha, Özgun Babur, Chris Sander, Augustin Luna
Peer Reviewers Ruth Isserlin; Katsuyuki Yugi
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 14 Nov 2022
https://doi.org/10.12688/f1000research.52460.1
Software Tool Article metrics
scNetViz: from single cells to networks using Cytoscape
[version 1; peer review: 2 approved]
Krishna Choudhary, Elaine C. Meng, J. Javier Diaz-Mejia, Gary D. Bader, Alexander R. Pico, John H. Morris
Peer Reviewers Luca Pinello; Kenji Kamimoto
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.26429.2
Software Tool Article metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.20887.3
Software Tool Article metrics
Revised
RCy3: Network biology using Cytoscape from within R
[version 3; peer review: 3 approved]
Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Peer Reviewers James Denvir; Krithika Bhuvaneshwar; Ludwig Geistlinger
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.14613.2
Software Tool Article metrics
Revised
CyTargetLinker app update: A flexible solution for network extension in Cytoscape
[version 2; peer review: 2 approved]
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
Peer Reviewers Alex Gutteridge; John H. Morris
  • Funders
  • ELIXIR
  • Dutch Province of Limburg
LATEST VERSION PUBLISHED 13 Aug 2019
https://doi.org/10.12688/f1000research.19592.1
Software Tool Article metrics
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
[version 1; peer review: 3 approved]
Aurora S. Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
Peer Reviewers Fuhai Li; Aritro Nath; Tero Aittokallio and Ziaurrehman Tanoli
  • Funder
  • National Institutes of Health
PUBLISHED 20 Jun 2019
https://doi.org/10.12688/f1000research.15146.2
Software Tool Article metrics
Revised
aMatReader: Importing adjacency matrices via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Hideo Matsuda; Kimberly Glass
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.15144.2
Software Tool Article metrics
Revised
Copycat Layout: Network layout alignment via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Bernhard Mlecnik; Katja Luck
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.14807.2
Software Tool Article metrics
Revised
Identifier Mapping in Cytoscape
[version 2; peer review: 3 approved]
Adam Treister, Alexander R. Pico
Peer Reviewers Ruth Isserlin; Augustin Luna; Nadezhda Doncheva
  • Funder
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 06 Aug 2018
https://doi.org/10.12688/f1000research.14612.2
Software Tool Article metrics
Revised
eXamine: Visualizing annotated networks in Cytoscape
[version 2; peer review: 4 approved]
Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
Peer Reviewers Barry Demchak; Richa Batra; Markus List; Alexander Pico
LATEST VERSION PUBLISHED 05 Jul 2018
https://doi.org/10.12688/f1000research.14298.2
Software Tool Article metrics
Revised
Comparing protein structures with RINspector automation in Cytoscape
[version 2; peer review: 3 approved]
Guillaume Brysbaert, Théo Mauri, Marc F. Lensink
Peer Reviewers Sjoerd J. de Vries; Turkan Haliloglu and Ezgi Karaca; Rita Casadio
LATEST VERSION PUBLISHED 22 Jun 2018
https://doi.org/10.12688/f1000research.15355.1
Editorial metrics NOT PEER REVIEWED
The Cytoscape Automation app article collection
[version 1; peer review: not peer reviewed]
Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H Morris, William Longabaugh, Christian Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
PUBLISHED 20 Jun 2018
https://doi.org/10.12688/f1000research.14616.1
Software Tool Article metrics
Automating the PathLinker app for Cytoscape
[version 1; peer review: 2 approved]
Li Jun Huang, Jeffrey N. Law, T. M. Murali
Peer Reviewers Alexander Pico; Stefan Wuchty
  • Funders
  • Intelligence Advanced Research Projects Activity
  • National Science Foundation
PUBLISHED 12 Jun 2018
https://doi.org/10.12688/f1000research.14810.1
Software Tool Article metrics
autoHGPEC: Automated prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network
[version 1; peer review: 2 approved with reservations]
Duc-Hau Le, Trang T.H. Tran
Peer Reviewers Tin Nguyen; Thanh Le Van
PUBLISHED 24 May 2018
https://doi.org/10.12688/f1000research.14776.2
Software Tool Article metrics
Revised
Automation of ReactomeFIViz via CyREST API
[version 2; peer review: 2 approved]
Fred Loney, Guanming Wu
Peer Reviewers Marina Piccirillo; John H. Morris
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 23 May 2018
https://doi.org/10.12688/f1000research.9203.3
Software Tool Article metrics
Revised
Creating, generating and comparing random network models with NetworkRandomizer
[version 3; peer review: 2 approved, 1 approved with reservations]
Gabriele Tosadori, Ivan Bestvina, Fausto Spoto, Carlo Laudanna, Giovanni Scardoni
Peer Reviewers Giovanni Micale; Francesco Russo; Ankush Sharma
LATEST VERSION PUBLISHED 10 Nov 2017
https://doi.org/10.12688/f1000research.9751.2
Software Tool Article metrics
Revised
dot-app: a Graphviz-Cytoscape conversion plug-in
[version 2; peer review: 4 approved]
Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak
Peer Reviewers Eric Bonnet; Matthias König; David J. Lynn and John Salamon; Giovanni Scardoni
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 10 Jul 2017
1-20 of 54 ARTICLES
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Gateway Areas
  • Automation
    Cytoscape Automation enables scripting languages (e.g., Python, R or Javascript) to call Cytoscape functions. These papers describe new callable functionality exposed in a number of highly used Cytoscape apps. Read more keyboard_arrow_right
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