The work with Shirley Pepke on using CorEx to find patterns in gene expression data is finally published in BMC Medical Genomics.
The code we used for the paper is online. I’m excited to see what people discover with these techniques, but I also can see we have more to do. If speed is an issue (it took us two days to run on a dataset with 6000 genes… many datasets can have an order of magnitude more genes), please get in touch as we have some experimental versions that are faster. We are also working on making the entire analysis pipeline more automated (i.e. connecting discovered factors with known biology and visualizing predictive factors.) To that end, I want to thank the Kestons for supporting future developments under the Michael and Linda Keston Executive Directorship Endowment.