GEPAS (Gene Expression Pattern Analysis Suite) - an experiment-oriented pipeline for the analysis of microarray gene expression data. It contains an incredible number of tools for normalization, preprocessing, viewing, clustering, differential expression, supervised classification, and data mining & analysis. (Reference: J.M. Vaquerizas et al. 2005. Nucl. Acids Res. 33: W616-W620).

Cyber-T (National Center for Genomic Resources, U.S.A.) if you have 2-dye data (such as what would be generated by the usual glass slide arrays probed with cy3/cy5-labelled cDN) use PAIRED DATA, while Control+Experimental is for those with Affymetrix-based data consisting of a separate control and experimental arrays.

NIA Array Analysis Tool - for microarray data analysis, which features the false discovery rate for testing statistical significance and the principal component analysis using the singular value decomposition method for detecting the global trends of gene-expression patterns. Additional features include: analysis of variance with multiple methods for error variance adjustment, correction of cross-channel correlation for two-color microarrays, identification of genes specific to each cluster of tissue samples, biplot of tissues and corresponding tissue-specific genes, clustering of genes that are correlated with each principal component (PC), and three-dimensional graphics. (Reference: A.A. Sharov et al. 2005. Bioinformatics 21: 2548-2549).

MicroArray Genome Imaging & Clustering Tool (MAGIC Tool) - A JAVA teaching resource developed at Davidson College (U.S.A.) by Laurie Heyer and her undergraduate students (Reference: L. J. Heyer et al. 2005. Bioinformatics 21: 2114 - 2115).

GEMS - Gene Expression Module Sampler - simple but promising new approach for biclustering based on a Gibbs sampling paradigm. (Reference: C.-J. Wu et al. 2004. Genome Informatics 15: 239-248).  

 TRAPID is an online tool for the fast, reliable and user-friendly analysis of de novo transcriptomes. Through a highly optimized processing pipeline the TRAPID system offers functional and comparative analyses for transcriptome data sets. TRAPID is highly competitive with respect to other existing solutions with regards to both speed and quality. (Reference: Van Bel M. et al. Genome Biol. 2013;14(12):R134).

 TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. N.B. Requires registration. (Reference: Kornobis E et al (2015) Evol Bioinform Online 11:97-104).

 Chipster is a user-friendly software for analyzing high-throughput data such as NGS and microarrays. It contains over 360 analysis tools and a large collection of reference genomes.  Conditions for use are listed under Getting access