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https://doi.org/10.12688/f1000research.9909.1
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The PathLinker app: Connect the dots in protein interaction networks
[version 1; peer review: 1 approved, 2 approved with reservations]
Daniel P. Gil, Jeffrey N. Law, T. M. Murali
Peer Reviewers Barry Demchak; Tamás Korcsmáros and David Fazekas; Stefan Wuchty
  • Funders
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 20 Jan 2017
https://doi.org/10.12688/f1000research.9050.2
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Revised
CoNet app: inference of biological association networks using Cytoscape
[version 2; peer review: 2 approved]
Karoline Faust, Jeroen Raes
Peer Reviewers Paul Wilmes and Anna Heintz-Buschart; Alexander Eiler
LATEST VERSION PUBLISHED 14 Oct 2016
https://doi.org/10.12688/f1000research.9118.2
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Revised
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
[version 2; peer review: 2 approved]
Tanja Muetze, Ivan H. Goenawan, Heather L. Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J. Lynn
Peer Reviewers Sandra Orchard and Pablo Porras Millán; Christopher K. Tuggle and Haibo Liu
LATEST VERSION PUBLISHED 30 Aug 2016
https://doi.org/10.12688/f1000research.9211.1
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cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK
[version 1; peer review: 2 approved with reservations]
Matthias König
Peer Reviewers Barry Demchak; Ali Salehzadeh-Yazdi
PUBLISHED 18 Jul 2016
https://doi.org/10.12688/f1000research.9090.1
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AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
[version 1; peer review: 2 approved]
Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader
Peer Reviewers Pablo Porras Millán; Harm Nijveen
PUBLISHED 15 Jul 2016
https://doi.org/10.12688/f1000research.9130.1
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webANIMO: Improving the accessibility of ANIMO
[version 1; peer review: 3 approved with reservations]
Willem Siers, Michiel Bakker, Bob Rubbens, Ruben Haasjes, Jacco Brandt, Stefano Schivo
Peer Reviewers Denis Thieffry and Céline Hernandez; Gary D Bader and Rosario Distefano; Aurélien Naldi
PUBLISHED 15 Jul 2016
https://doi.org/10.12688/f1000research.9184.1
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SCODE: A Cytoscape app for supervised complex detection in protein-protein interaction graphs
[version 1; peer review: 2 approved with reservations]
Sarah Mohamed, Nick Janus, Yanjun Qi
Peer Reviewers Narayanaswamy Srinivasan; T.M. Murali
PUBLISHED 14 Jul 2016
https://doi.org/10.12688/f1000research.9054.1
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Robust de novo pathway enrichment with KeyPathwayMiner 5
[version 1; peer review: 2 approved]
Nicolas Alcaraz, Markus List, Martin Dissing-Hansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Henrik J. Ditzel, Jan Baumbach
Peer Reviewers Alberto Calderone; Mona Riemenschneider
PUBLISHED 28 Jun 2016
https://doi.org/10.12688/f1000research.8402.1
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CyLineUp: A Cytoscape app for visualizing data in network small multiples
[version 1; peer review: 2 approved]
Maria Cecília D. Costa, Thijs Slijkhuis, Wilco Ligterink, Henk W.M. Hilhorst, Dick de Ridder, Harm Nijveen
Peer Reviewers Alexander R Pico; Oren Tzfadia
PUBLISHED 11 Apr 2016
https://doi.org/10.12688/f1000research.6769.2
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Revised
Finding the shortest path with PesCa: a tool for network reconstruction
[version 2; peer review: 2 approved, 2 approved with reservations]
Giovanni Scardoni, Gabriele Tosadori, Sakshi Pratap, Fausto Spoto, Carlo Laudanna
Peer Reviewers Ferenc Jordán; Ankush Sharma; Anna Zhukova; Salvatore Alaimo
LATEST VERSION PUBLISHED 07 Apr 2016
https://doi.org/10.12688/f1000research.6852.2
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Revised
CyAnimator: Simple Animations of Cytoscape Networks
[version 2; peer review: 3 approved]
John H. Morris, Dhameliya Vijay, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
Peer Reviewers Giovanni Scardoni; Nathan Salomonis; Piet Molenaar
LATEST VERSION PUBLISHED 30 Dec 2015
https://doi.org/10.12688/f1000research.6804.3
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Revised
Social Network: a Cytoscape app for visualizing co-authorship networks
[version 3; peer review: 1 approved, 2 approved with reservations]
Victor Kofia, Ruth Isserlin, Alison M.J. Buchan, Gary D. Bader
Peer Reviewers Michael Bales and Terrie Wheeler; Jiang Bian; Shahadat Uddin
LATEST VERSION PUBLISHED 23 Dec 2015
https://doi.org/10.12688/f1000research.6656.2
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Revised
NetMatchStar: an enhanced Cytoscape network querying app
[version 2; peer review: 2 approved]
Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Peer Reviewers Xifeng Yan; Shaillay Dogra
LATEST VERSION PUBLISHED 03 Nov 2015
https://doi.org/10.12688/f1000research.6836.2
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Revised
iCTNet2: integrating heterogeneous biological interactions to understand complex traits
[version 2; peer review: 2 approved]
Lili Wang, Daniel S. Himmelstein, Adam Santaniello, Mousavi Parvin, Sergio E. Baranzini
Peer Reviewers Amitabh Sharma; Gary D Bader
LATEST VERSION PUBLISHED 28 Sep 2015
https://doi.org/10.12688/f1000research.6767.1
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CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
[version 1; peer review: 2 approved]
Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
Peer Reviewers Sergey Nepomnyachiy; Guanming Wu
PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.6773.1
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SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks
[version 1; peer review: 2 approved]
Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards
Peer Reviewers Ulrich Stelzl; Srikrishna Subramanian and Gurmeet Kaur
PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.4392.2
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setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges
[version 2; peer review: 3 approved]
John H. Morris, Samad Lotia, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Alexander R. Pico, Thomas E Ferrin
Peer Reviewers Jiguang Wang; Thomas Kelder; Tamara Munzner
LATEST VERSION PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.6797.1
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CySpanningTree: Minimal Spanning Tree computation in Cytoscape
[version 1; peer review: 1 approved, 1 approved with reservations]
Faizaan Shaik, Srikanth Bezawada, Neena Goveas
Peer Reviewers Shaillay Dogra; Ankush Sharma
PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.4477.2
Software Tool Article metrics
Revised
Biological network analysis with CentiScaPe: centralities and experimental dataset integration
[version 2; peer review: 2 approved]
Giovanni Scardoni, Gabriele Tosadori, Mohammed Faizan, Fausto Spoto, Franco Fabbri, Carlo Laudanna
Peer Reviewers Ferenc Jordan; Ankush Sharma
LATEST VERSION PUBLISHED 07 Jul 2015
https://doi.org/10.12688/f1000research.4510.2
Software Tool Article metrics
Revised
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters
[version 2; peer review: 2 approved]
Keiichiro Ono, Barry Demchak, Trey Ideker
Peer Reviewers Alexander Lex; Jose Villaveces
LATEST VERSION PUBLISHED 28 Oct 2014
21-40 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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