J-Express:Web based application that runs many different types of methods for calculating differential gene expression, including rank product, SAM and GSEA. It also runs easy clustering and PCA analysis.

MeV: Desktop application for the analysis, visualization and data-mining of large-scale genomic expression data. Only for Windows.

VAMPIRE: Java based integrated environment for performing several levels of gene expression microarray analysis.

R and bioconductor based packages:

·   RPA: Robust probabilistic averaging. Package for probe reliability analysis and gene expression preprocessing.

·   affy: Methods for Affymetrix Oligonucleotide Arrays

·   AffylmGUI: GUI for affy analysis using limma Package

·   samr:Significance Analysis of Microarrays

·   Limma: linear Models for Microarray data

   limmaGUI: Graphical User Interface for the limma Microarray package. Only for two-colour array.

·   OneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

·   RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis

·   maSigPro: Significant Gene Expression Profile Differences in Time Course Microarray Data