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. 2014 Mar 20;9(3):e90801. doi: 10.1371/journal.pone.0090801

Table 1. The class and availability of biclustering methods.

Bicluster Method Class Since Availability Parameters
ACV [50] CMB 2007 - Inline graphic, Inline graphic
Bayesian Plaid [51], [52] PGM 2008 C [52] Inline graphic
Bimax [11] VMB 2006 Java [53] Inline graphic
BiMine [46] CMB 2009 Java Inline graphic, Inline graphic
CC [7] CMB 2000 R [54], Java [53] Inline graphic
CMonkey [9] PGM 2006 R Inline graphic
CTWC [19] TWC 2000 MATLAB Inline graphic
DCC [55], [56] TWC 2002 - -
FABIA and FABIAS [21] PGM 2010 R Inline graphic
FLOC [14] CMB 2005 R Inline graphic
GEMS [57], [58] CGS 2004 Web, C Inline graphic
Gibbs biclustering [12] PGM 2003 - -
ISA [43], [44] TWC 2002 Java [53] Inline graphic
ITWC [20] TWC 2001 - -
OP-Clustering [59], [60] CMB 2003 - -
OPSM [40] CMB 2003 Java [53], C# Inline graphic
Plaid [41], [42] PGM 2002 R [54], web Inline graphic
ProBic [22] PGM 2009 - -
QUBIC [45] VMB 2009 C Inline graphic, Inline graphic, Inline graphic
R/MSBE [30] VMB 2006 Java Inline graphic
SAMBA [13] PGM 2002 Java [61] Inline graphic
Spectral [62] VMB 2003 R [54] Inline graphic
TreeBic [49] PGM 2010 C Inline graphic
UBCLUST [63] CMB 2006 Java Inline graphic
XMOTIF [15] VMB 2003 R [54], C, Java [53] Inline graphic
ZBDD [18] VMB 2005 - Inline graphic
Inline graphic -clustering [16] VMB 1972 - Inline graphic
Inline graphic -Pclustering [17] VMB 2002 - Inline graphic
Inline graphic -jk [64] VMB 2000 - Inline graphic, Inline graphic

The notations used for the methods classes are stated in the text. The parameters used by the biclustering methods are described in Table 4. The methods that are shown in bold texts were evaluated in our study.