Sites of Note

Software Projects


Gene Signature Database is a searchable database of manually curated gene expression signatures which we have collected from the literature. Release 4.0 (Sep 2011) contains over 2,00 gene signature which focus on cancer, viral and stem cell gene signatures.


made4 is a Bioconductor package which I develop and maintain. made4 is an extension to ade4, and provides functions to perform between group analysis, coinertia analysis and other methods we have described. It provides many visualization functions, including heatplot (adapted heatmap which includes a scale bar and sample/gene color bar), pretty.dend  (dendrogram with covariate colorbars), and functions to view the results of prinipcal component analysis or correspondence analysis in 1D, 2D or 3D plots.

Gene Expression Atlas (GXA)

GXA is an excellent resource which takes data from the public microarray and RNA-seq data repositories, normalizes the raw data and perform statistical analysis including moderated t-tests on each phenotype in each dataset. In Release 11 (Sep 2011) they over 5,500 studies with greater than 135,000 samples on 18 species.  We have been collaborating with Misha Kapushesky and his team at the EBI on integrating Gene Set Analysis and linking GeneSigDB to GXA


The Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute

The Women’s Cancer Program at Dana-Farber Cancer Institute

Research Groups

The Computational Biology and Functional Genomics Laboratory– See more about the projects I am working on in Prof. John Quackenbush’s Computational Biology and Functional Genomics Laboratory at Dana-Farber Cancer Institute.  John explains how computational biology is being used to advance cancer research at DFCIOpens in New Window

Prof Des Higgins, Conway Institute, University College Dublin, Ireland – I am collaborating with Prof Des Higgins (UCD) in the development and application of multivariate methods for the analysis of high throughout genomic and proteomic data.  Des plays guitarOpens in New Window