Table 3.

Overview of public software tools for predictive model building, clustering analysis and dimension reduction and visualization of omics data

Method type	Software name	Availability	Supported featuresa	Web application	Reference
Multi-purpose machine-learning analysis tool sets	CARMAWeb	https://carmaweb.genome.tugraz.at/carma/	N, P, C, D, V	Yes	Rainer et al. 2006
	ArrayMining	http://www.arraymining.net	N, P, C, D, V	Yes	Glaab et al. 2009
	mixOmics	https://cran.r-project.org/web/packages/mixOmics	P, D, V	No	Rohart et al. 2017
	Weka	http://www.cs.waikato.ac.nz/ml/weka	P, C, D, V	No	Hall et al. 2009
	Orange	https://orange.biolab.si	P, C, D, V	No	Demšar et al. 2013
	CMA	https://bioconductor.org/packages/release/bioc/html/CMA.html	P, D, V	No	Slawski et al. 2008
	MLSeq	https://bioconductor.org/packages/release/bioc/html/MLSeq.html	P, D	No	Zararsiz et al. 2014
Tools centered around feature ranking/feature selection	Limma	https://bioconductor.org/packages/release/bioc/html/limma.html	N, D, V	No	Smyth 2005
	RankProd	https://bioconductor.org/packages/release/bioc/html/RankProd.html	D, V	No	Hong et al. 2006
	ArrayPipe	http://www.pathogenomics.ca/arraypipe	N, D, V,	Yes	Hokamp et al. 2004
	RAP	https://bioinformatics.cineca.it/rap	N, D, V	Yes	D’Antonio et al. 2015
	EzArray	http://ezarray.com	N, D, V	Yes	Natale et al. 2014
Tools for low-dimensional data visualization	GGobi	http://www.ggobi.org	D, V	No	Temple Lang and Swayne 2001
	PlotViz	http://salsahpc.indiana.edu/plotviz	D, V	No	Choi et al. 2010
	RnavGraph	https://cran.r-project.org/web/packages/RnavGraph	V	No	Waddell and Oldford 2011
	Arena3D	http://arena3d.org	V	No	Secrier et al. 2012

^aColumn 3 highlights the supported features of the tools using the following codes: N normalization/preprocessing, P predictive model building, C unsupervised clustering, D dimension reduction (variable selection or feature transformation), V visualization. Tools available as web applications are highlighted in column 4