Whole-genome expression profiling has created a revolution in the way we study disease and basic biology. Since 1997, the number of published results based on an analysis of gene expression microarray data has grown from 30 to over 5,000 publications per year. Sophisticated mathematical methods have been developed for use in patient diagnosis and prognosis, identification of new drug targets and understanding biological mechanisms. However, these tools are often out of the direct reach of the biomedical researchers who can so critically benefit from them because they can be difficult to understand and use correctly. This challenge is even more relevant in the context of ‘integrative’approaches, where a multitude of data sources and methods are combined in the analysis of a single problem. To address this challenge in genomics research we have developed a software package called GenePattern (see the Supplementary Tutorial and list of frequently asked questions in the Supplementary Note online), which provides a comprehensive environment that can support (i) a broad community of users at all levels of computational experience and sophistication,(ii) access to a repository of analytic and visualization tools and easy creation of complex analytic methods from them and (iii) the rapid development and dissemination of new methods.