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Table 1 Arena3D versus previous version

From: Arena3D: visualizing time-driven phenotypic differences in biological systems

Functionality

Previous versions

Arena3D 2.0

Load network data

x

x

Load time course data

 

x

Layouts

  

Circular

x

x

Grid

x

x

Spherical

x

x

Hierarchical

x

x

Clustering

  

Fruchterman - Reingold

x

x

Distance Geometry

x

x

Affinity Propagation

x

x

Markov Clustering

x

x

K-Means

x

x

Neighbor Joining

x

x

UPGMA

x

x

Move nodes

x

x

Move/scale/spin layers

x

x

Time course data analysis

  

Time slider

 

x

Cluster by gene expression

 

x

Highlight peaks

 

x

Cluster by top expression changes

 

x

Play animation

 

x

Individual gene tracking

 

x

Pearson/Spearman correlation display

 

x

Similarity scoring

 

x

Choose color scheme

 

x

Colorblind-safe color scheme

 

x

Network export

  

Medusa format

x

x

Pajek format

x

x

VRML format

x

x

JPEG format

x

x

  1. Listed are the different functionality improvements with respect to the previous version of the software.