Available software for meta-analyses of genome-wide expression studies

Advances in transcriptomic methods have led to a large number of published genome-wide expression studies (GWES), in humans and in model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, I review the main features of available software for carrying out meta-analysis of GWES. I describe seven packages from the Bioconductor platform and 5 packages from the CRAN platform. In addition, nine previously described programs and two online programs are reviewed. Finally, I discuss advantages and disadvantages of these available programs and propose key points for future developments.