ISMAGS 1.1.3 – Cytoscape app for Motif Enumeration

ISMAGS 1.1.3

:: DESCRIPTION

ISMAGS (InStances of a Motif in A Graph) can numerate all instances of a motif in a graph, making optimal use of the motif’s symmetries.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java
  • Cytoscape

:: DOWNLOAD

ISMAGS

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 1;33(3):461-463. doi: 10.1093/bioinformatics/btw626.
A Cytoscape app for motif enumeration with ISMAGS.
Van Parys T, Melckenbeeck I, Houbraken M, Audenaert P, Colle D, Pickavet M, Demeester P, Van de Peer Y

Cytoscape 3.7.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.7.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

eXamine 2.1.2 – Cytoscape app for Exploring Annotated Modules in Nnetworks

eXamine 2.1.2

:: DESCRIPTION

eXamine is a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. eXamine extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours.

::DEVELOPER

Centrum Wiskunde & Informatica (CWI)

:: SCREENSHOTS

eXamine

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 eXamine

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jul 10;15:201. doi: 10.1186/1471-2105-15-201.
eXamine: exploring annotated modules in networks.
Dinkla K, El-Kebir M, Bucur CI, Siderius M, Smit MJ, Westenberg MA1, Klau GW.

PetriScape 1.0 – Plugin for discrete Petri net simulations in Cytoscape

PetriScape 1.0

:: DESCRIPTION

PetriScape is a tool for discrete Petri net simulation of biological networks in Cytoscape.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

PetriScape

:: MORE INFORMATION

Citation

J Integr Bioinform. 2016 Jun 4;13(1):284. doi: 10.2390/biecoll-jib-2016-284.
PetriScape – A plugin for discrete Petri net simulations in Cytoscape.
Almeida D, Azevedo V, Silva A, Baumbach J.

GEDEVO / GEDEVO-M / CytoGEDEVO 1.0.3.1 – Global Alignment of Biological Networks with Cytoscape

GEDEVO / GEDEVO-M / CytoGEDEVO 1.0.3.1

:: DESCRIPTION

GEDEVO (Graph Edit Distance + EVOlution) is a software tool for solving the network alignment problem.

GEDEVO-M is an extension of the idea implemented in GEDEVO to multiple input networks.

CytoGEDEVO is a Cytoscape plugin that implements the GEDEVO  method for pairwise global network alignment.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

CytoGEDEVO

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 GEDEVO /  GEDEVO-MCytoGEDEVO

:: MORE INFORMATION

Citation

Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach:
GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment.
GCB 2013:68-79

CytoGEDEVO – Global alignment of biological networks with Cytoscape.
Malek M, Ibragimov R, Albrecht M, Baumbach J.
Bioinformatics. 2015 Dec 14. pii: btv732

CytoscapeRPC 1.8 – Create, Query and Modify Cytoscape Networks

CytoscapeRPC 1.8

:: DESCRIPTION

CytoscapeRPC is a Cytoscape plug-in which allows users to create, query and modify Cytoscape networks. This means that you can automate your Cytoscape tasks from any programming language which supports XML-RPC

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CytoscapeRPC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2451-2. Epub 2011 Jun 27.
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.
Bot JJ, Reinders MJ.

ReNE 1.9 – A Cytoscape Plugin for Regulatory Network Enhancement

ReNE 1.9

:: DESCRIPTION

ReNE plugin, is a new Cytoscape 3.x plugin, which enables integration, merging, enhancement, visualization, and exporting of pathways from multiple repositories.

::DEVELOPER

The SysBIO research group

:: SCREENSHOTS

ReNE

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • Cytoscape

:: DOWNLOAD

 ReNE

:: MORE INFORMATION

Citation

PLoS One. 2014 Dec 26;9(12):e115585. doi: 10.1371/journal.pone.0115585. eCollection 2014.
ReNE: a cytoscape plugin for regulatory network enhancement.
Politano G, Benso A, Savino A, Di Carlo S.

clusterMaker2 0.9.5 – Creat and Visualize Cytoscape Clusters

clusterMaker2 0.9.5

:: DESCRIPTION

UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

clusterMaker

:: REQUIREMENTS

:: DOWNLOAD

 clusterMaker

:: MORE INFORMATION

Citation:

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.
BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

enhancedGraphics 1.0.3 – Cytoscape app for enhanced Node Graphics

enhancedGraphics 1.0.3

:: DESCRIPTION

enhancedGraphics is a Cytoscape app that implements a series of enhanced charts and graphics that may be added to Cytoscape nodes.

::DEVELOPER

enhancedGraphics team

:: SCREENSHOTS

enhancedGraphics

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 enhancedGraphics

:: MORE INFORMATION

Citation

enhancedGraphics: a Cytoscape app for enhanced node graphics.
Morris JH, Kuchinsky A, Ferrin TE, Pico AR.
F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1

PINBPA 1.1.8 – Cytoscape app for Network Analysis of GWAS data

PINBPA 1.1.8

:: DESCRIPTION

PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.

::DEVELOPER

PINBPA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 PINBPA

:: MORE INFORMATION

Citation

PINBPA: Cytoscape app for network analysis of GWAS data.
Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini S.
Bioinformatics. 2014 Sep 25. pii: btu644