ModuleNetworkTools

The table below presents a comparison of features and application domains of all available module network software tools that we are aware of, in chronological order by their first release date.

Legend:

• I/O: g, graphical user interface; c, command line.
• Source: source code available, yes or no.
• Data: supported data integration; m, mRNA expression; mi, microRNA expression; e, eQTL data; c, CNV data; p, protein interactions; m-s, mRNA expression multiple species; any, any combination of discrete or continuous datatypes measured on the same samples.

Software	Language	I/O	Source	Data	URL	Year
Genomica	Java	g	no	m	http://genomica.weizmann.ac.il	2003
Geronemo	Java	g	no	m, e	http://ai.stanford.edu/~koller/index.html	2006
LeMoNe	Java/Matlab	c	yes	m, mi	http://bioinformatics.psb.ugent.be/software/details/LeMoNe	2007
Lirnet	Matlab	c	yes	m, e	http://homes.cs.washington.edu/~suinlee/lirnet	2009
CONEXIC	Java	c	no	m, c	http://www.c2b2.columbia.edu/danapeerlab/html/conexic.html	2010
PMN	Unix binary	c	no	m, p	http://www.compbio.cs.huji.ac.il/PMN	2010
ARBORETUM	C	c	yes	m-s	http://pages.discovery.wisc.edu/~sroy/arboretum	2013
MERLIN	C	c	yes	m	http://pages.discovery.wisc.edu/~sroy/merlin	2013
Lemon-Tree	Java	c	yes	m, mi, e, c, any	http://lemon-tree.googlecode.com	2014