Tag: EDGE

setsApp 2.2.0 – Save and Manipulate Sets of Nodes and Edges

setsApp 2.2.0

:: DESCRIPTION

SetsApp is a Cytoscape 3 app allowing the user to create and manipulate sets of nodes or edges (but not sets with both nodes and edges, at least in the current version) in Cytoscape. Sets can be created for different networks.

::DEVELOPER

setsApp team

:: SCREENSHOTS

setsApp

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 SetsApp

:: MORE INFORMATION

Citation

setsApp: Set operations for Cytoscape Nodes and Edges.
Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE.
F1000Res. 2014 Jul 1;3:149. doi: 10.12688/f1000research.4392.1.

CyToStruct 0.2.5.2 – Launching Arbitrary External Apps (such as Viewers) for Nodes/Edges

CyToStruct 0.2.5.2

:: DESCRIPTION

CyToStruct is a Cytoscape app for executing external applications in command or batch mode. CyToStruct allows the user to define simple yet expressive rules for executing external applications by clicking on a context menu of a node/edge.

::DEVELOPER

Rachel Kolodny

:: SCREENSHOTS

CyToStruct

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 CyToStruct

:: MORE INFORMATION

Citation:

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers.
Nepomnyachiy S, Ben-Tal N, Kolodny R.
Structure. 2015 Apr 3. pii: S0969-2126(15)00076-3. doi: 10.1016/j.str.2015.02.013

EDGE 2.22.0 – Extraction of Differential Gene Expression

EDGE 2.22.0

:: DESCRIPTION

EDGE is a software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology

::DEVELOPER

Jeffrey Leek, Alan Dabney, Eva Monsen and John Storey.

:: SCREENSHOTS

EDGE

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R
  • BioConductor

:: DOWNLOAD

EDGE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 15;27(4):509-15. doi: 10.1093/bioinformatics/btq701. Epub 2010 Dec 24.
A computationally efficient modular optimal discovery procedure.
Woo S, Leek JT, Storey JD.