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