RNA

Regulatory Network Analyzer generates/analyzes a regulatory network and states transition network and computes informations like entropy.
RNA takes as entry an interaction network, represented by a file of **.txt** format. That file must contain a matrix of size **n** x **n**, where **n** is the number of genes/nodes. The entry file shoud follow the notation: - The first row contain the names of the genes, separated by comma (,); -The following lines contain one of the following: 1: when the gene j is activated by the gene i; 0: when there is no interaction between i and j; -1: when the gene j is inhibited by gene i; - The numbers are also separated by comma (,). Here goes an example of matrix of the **yeast cell-cycle network**: Cln3,MBF,SBF,Cln12,Cdh1,Swi5,Cdc20,Clb56,Sic1,Clb12,Mcm1 -1,0,0,0,0,0,0,0,0,0,0 1,0,0,0,0,0,0,0,0,-1,0 1,0,0,0,0,0,0,0,0,-1,0 0,0,1,-1,0,0,0,0,0,0,0 0,0,0,-1,0,0,1,-1,0,-1,0 0,0,0,0,0,-1,1,0,0,-1,1 0,0,0,0,0,0,-1,0,0,1,1 0,1,0,0,0,0,-1,0,-1,0,0 0,0,0,-1,0,1,1,-1,0,-1,0 0,0,0,0,-1,0,-1,1,-1,0,1 0,0,0,0,0,0,0,1,0,1,-1 Using the entry file, we generate the matrix visualization as a cytoscape network. Along with that visualization we also generate a state transition network, that contains 2^n nodes, *so is possible that cytoscape will crash for regulatory networks with more than 20 nodes* (2^20), the layout of the network also affects the performance, by default the layout selected is *Grid Layout*, the grid layout was selected because of some tests of performance made. Each basin of attraction of the network has a different color. The app also computes some information from the states transition network like the **entropy** and the **derrida coefficient**. These informations are shown in the results panel. ###Bug Reports If you find a bug, please file a report at [https://github.com/Sibelly/rna-app/issues GitHub Issues].

1.0.4

Works with Cytoscape 3.3

Release Notes

Correcting the label " Number of interactions" to "Sampling Rate".

1.0.3

Works with Cytoscape 3.3

Release Notes

The default layout was changed from the Hierarchical to the Grid Layout after some performance tests made.

1.0.2

Works with Cytoscape 3.3


1.0.1

Works with Cytoscape 3.3


1.0.0

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 1.0.4

Released 15 Apr 2016

Works with Cytoscape 3.3

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