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Cytoscape

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41-54 of 54 ARTICLES
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https://doi.org/10.12688/f1000research.4537.2
Software Tool Article metrics
Revised
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks
[version 2; peer review: 2 approved, 1 approved with reservations]
Giovanni Micale, Andrea Continella, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti
Peer Reviewers Antonio J. Perez Pulido and Pablo Mier; Rintaro Saito; Byung-Jun Yoon and Pablo Mier
LATEST VERSION PUBLISHED 23 Sep 2014
https://doi.org/10.12688/f1000research.4431.2
Software Tool Article metrics
Revised
ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis
[version 2; peer review: 2 approved]
Guanming Wu, Eric Dawson, Adrian Duong, Robin Haw, Lincoln Stein
Peer Reviewers Hamid Bolouri; Nikolaus Schultz and B. Arman Aksoy
LATEST VERSION PUBLISHED 12 Sep 2014
https://doi.org/10.12688/f1000research.4254.2
Software Tool Article metrics
Revised
WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization
[version 2; peer review: 2 approved]
Martina Kutmon, Samad Lotia, Chris T. Evelo, Alexander R Pico
Peer Reviewers Christian A Grove; Ted Goldstein
LATEST VERSION PUBLISHED 11 Sep 2014
https://doi.org/10.12688/f1000research.4492.2
Software Tool Article metrics
Revised
Cytoscape: the network visualization tool for GenomeSpace workflows
[version 2; peer review: 3 approved]
Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael Smoot, Trey Ideker, Jill P. Mesirov
Peer Reviewers Aris Floratos; Gabriela Bindea and Bernhard Mlecnik; Jan Aerts
LATEST VERSION PUBLISHED 26 Aug 2014
https://doi.org/10.12688/f1000research.4410.2
Software Tool Article metrics
Revised
CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows
[version 2; peer review: 2 approved]
Lilit Nersisyan, Ruben Samsonyan, Arsen Arakelyan
Peer Reviewers Hans Binder; Augustin Luna
LATEST VERSION PUBLISHED 14 Aug 2014
https://doi.org/10.12688/f1000research.4572.1
Software Tool Article metrics
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
[version 1; peer review: 2 approved]
Jason Montojo, Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
Peer Reviewers Giovanni Scardoni; Rosalba Giugno
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4546.1
Software Tool Article metrics
Porting and using PanGIA for Cytoscape 3: challenges and solutions
[version 1; peer review: 3 approved]
David Welker, Barry Demchak
Peer Reviewers Brian Kidd; Alfredo Pulvirenti; Christian Lopes
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4521.1
Software Tool Article metrics
BridgeDb app: unifying identifier mapping services for Cytoscape
[version 1; peer review: 2 approved]
Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
Peer Reviewers Benno Schwikowski; Olivier Elemento
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4460.1
Software Tool Article metrics
enhancedGraphics: a Cytoscape app for enhanced node graphics
[version 1; peer review: 2 approved]
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
Peer Reviewers Lars Juhl Jensen; Piet Molenaar
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4524.1
Software Tool Article metrics
KEGGscape: a Cytoscape app for pathway data integration
[version 1; peer review: 1 approved, 2 approved with reservations]
Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi
Peer Reviewers Matthew DeJongh; Egon Willighagen; Melissa Cline
  • Funder
  • Japan Science and Technology Agency
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4573.1
Software Tool Article metrics
Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks
[version 1; peer review: 2 approved]
Juan J. Diaz-Montana, Norberto Diaz-Diaz
Peer Reviewers Cristina Rubino Escudero; Alexander Pico
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4536.1
Software Tool Article metrics
Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results
[version 1; peer review: 2 approved]
Ruth Isserlin, Daniele Merico, Veronique Voisin, Gary D. Bader
Peer Reviewers Nathan Salomonis; Florian Markowetz
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.2-192.v2
Software Tool Article metrics
Revised
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
[version 2; peer review: 3 approved]
Emanuel Gonçalves, Franz Mirlach, Julio Saez-Rodriguez
Peer Reviewers Nikolaus Schultz and B. Arman Aksoy; Ghislain Bidaut; Paul T. Shannon
LATEST VERSION PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4642.1
Editorial metrics NOT PEER REVIEWED
The Cytoscape app article collection
[version 1; peer review: not peer reviewed]
Alexander R Pico, Gary D Bader, Barry Demchak, Oriol Guitart Pla, Timothy Hull, William Longabaugh, Christian Lopes, Samad Lotia, Piet Molenaar, Jason Montojo, John H Morris, Keiichiro Ono, Benno Schwikowski, David Welker, Trey Ideker
PUBLISHED 01 Jul 2014
41-54 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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