Usage: aracne [OPTION] ...

Standard ARACNe arguments:

	-i  <file>		Input gene expression profile dataset

	-o  <file>		Output file name (optional) [*]

	-j  <file>		Existing adjacency matrix (.adj) file

	-a  <fixed_bandwidth|variable_bandwidth|adaptive_partitioning> 	Algorithm (fixed_bandwidth|variable_bandwidth|adaptive_partitioning), default: fixed_bandwidth

	-k  <kernel width>  	Kernel width (accurate method only), default: determined by program

	-t  <threshold>     	MI threshold, default: 0

	-p  <p-value>       	P-value for MI threshold (e.g. 1e-7), default: 1 [**]	

	-e  <tolerance>     	DPI tolerance, default: 1

	-h  <probeId>       	Hub gene (only MI w/ hub gene will be computed), default: NONE

	-r  <sample number> 	Use resampling of arrays

	-s  <file>          	A file containing a list of probes for which a subnetwork will be
	                    	constructed, default: NONE

	-l  <file>          	A file containing a list of probes annotated as transcription 
				factors in the input dataset, default: NONE [***]

	-c  <+/-probeId %>	Conditional network reconstruction, default: NONE [****]
	                    	[format: "+24 0.35", "-1973_s_at 0.4"]
	
	-f  <mean> <cv>     	Gene filter by the mean and coefficient of variance (cv) of the
	                    	expression values, default: mean=0, cv=0
	
	-H  <ARACNE_HOME>	To specify where the ARACNE configuration files locates,
				default: current working directory   	

	--help              	Display this help and exit

[*]	If no output file is specified by the user, an output will be automatically generated in 
	the same directory as the input file by appending some of the parameter values, such as
	kernel width, MI threshold, tolerance and so on, at the end of the input file name, and
	changing the file extension to ".adj".

[**]	If the "-t" option is supplied, it will enforce the program to use the specified MI 
	threshold, therefore the "-p" option will be ignored. Otherwise, the program will 
	automatically determines the MI threshold given the p-value. The default, p-value=1, will
	preserve all pairwise MI. 

[***]	This option is ideal for transcriptional network reconstruction. If provided, DPI will not
	remove any connection of a transcription factor (TF) by connections between two probes not
	annotated as TFs. This option is often used in conjunction with '-s', which specifies a list
	of probes that are either the same or a subset of the probes specified by '-l'.  	


[****]	Conditional network reconstructs the network given a specified probe being most expressed or 
	least expressed. In the format that follows "-c", "probeId" indicate the probe to be 
	conditioned on; "+" or "-" specify whether the upper or lower tail of the probe's expression
	should be used as the condition, and "%" is a percentage between (0, 1) specifying the 
	proportion of samples used as the conditioning subset. 
	Example useage:"-c +24 0.35", "-c -1973_s_at 0.4".