MATLAB implementation of Brane Clust v1.0

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#  Author:																																															#
#   Pirayre Aurélie, aurelie.pirayre@ifpen.fr																														#
#																																																				#
#  Date:																																																#
#   May 17, 2016		    																																								#				
#																																																				#
#  References: [submitted to Bioinformatics]																														#	
#   [1] Aurélie Pirayre, Camille Couprie, Laurent Duval, and Jean-Christophe Pesquet	                  # 
#	   "BRANE Clust: cluster-assisted gene regulatory network inference refinement"   										#
#####_______________________________________________________________________________________________#####

%%%%% REQUIREMENTS and INSTALL %%%%%
  * You need some requirements to execute BRANE Cut: 
		- OS > Windows 7 
		- 64 bits
  * Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed version 7.16.  
  * If the MCR is not installed, download and install MCR Installer available at http://fr.mathworks.com/products/compiler/mcr/ 

%%%%% DREAM4 DEMO %%%%%
Required input arguments are:
 * Method: 'CLR' or 'GENIE3'     %[the input weights in an adjacency matrix]
 * beta: >1     %[the clustering influence parameter]
 * t: belong to [0,1]     %[the threshold parameter handling cluster fusion]
 * show: 0 or 1     %[if PR curves have to be saved in the results directory]

Usage with defaut parameter (Method = 'CLR', beta = 2, t = 0.8, show = 0)  
Go to the 'BRANEClust_demoDREAM4/distrib' directory, and use the following command: 	
	In the Windows console: BRANEClust_demoDREAM4.exe 
	 	or 
  In the Matlab prompt: system('BRANEClust_demoDREAM4.exe')

Usage with different parameters than defaut parameters: 
Go to the 'BRANEClust_demoDREAM4/distrib' directory, and use the following command: 	
	In the Windows console: BRANEClust_demoDREAM4.exe Method beta t show 
	 	or 
  In the Matlab prompt: system('BRANEClust_demoDREAM4.exe Method beta t show') 
where Method, beta, t and show are the desired parameter values

%%%%% Usage %%%%%
If you want to use BRANE Clust on your own data 

Required input arguments are:
 * Apath    %[the path of the input weights in an adjacency matrix]
 * TFpath     %[the path of the TF list: indices of TFs in the adjacency matrix, in column]
 * lambda: belong to [0,1]     %[the standard threshol parameter]
 * beta: >1     %[the clustering influence parameter]
 * t: belong to [0,1]     %[the threshold parameter handling cluster fusion]

____                                               ____                                   
___ Usage example to recover E.coli inferred network___ 
Parameter used : (lambda = 0.34, beta = 2, t = 0.3)

Go to the 'BRANEClust/distrib' directory, and use the following command: 	
	In the Windows console: BRANEClust.exe "..\data\DREAM5_GENIE3_Net3.mat" "..\data\DREAM5_Net3_TF.mat" 0.34 2 0.3 
	 	or 
  In the Matlab prompt: system('BRANEClust.exe ../data/DREAM5_GENIE3_Net3.mat ../data/DREAM5_Net3_TF.mat 0.34 2 0.3');

____            ____  
___ Generic usage___ 
Go to the 'BRANEClust/distrib' directory, and use the following command: 	
	In the Windows console: BRANEClust.exe Apath TFpath lambda beta t 
	 	or 
  In the Matlab prompt: system('BRANEClust.exe Apath TFpath lambda beta t');

%If parameters lambda, beta and t are not defined by the user, default values are used such that: lambda = 0.5, beta = 2 and t = 0.5;




