Gene-set analysis or GSA is a very popular analysis in bioinformatics. Currently available GSA approaches are based on univariate two-sample comparison of single genes. This means that they cannot test for differences in covariance structure between the two conditions. Yet interplay between genes is a central aspect of biological investigation and it is likely that such interplay may differ between conditions. The R package GGMGSA implements a novel approach for gene-set analysis that allows for truly multivariate hypotheses, in particular differences in gene-gene networks between conditions. For technical details of the approach we refer the reader to:
Städler, N. and Mukherjee, S. (2013). Network-based multivariate gene-set testing. Preprint arXiv:1308.2771.