MOTIVATION: The size and complex nature of mass spectrometry-based proteomics datasets motivate development of specialized software for statistical data analysis and exploration. We present DanteR, a graphical R package that features extensive statistical and diagnostic functions for quantitative proteomics data analysis, including normalization, imputation, hypothesis testing, interactive visualization and peptide-to-protein rollup. More importantly, users can easily extend the existing functionality by including their own algorithms under the Add-On tab. AVAILABILITY: DanteR and its associated user guide are available for download free of charge at http://omics.pnl.gov/software/. We have an updated binary source for the DanteR package up on our website together with a vignettes document. For Windows, a single click automatically installs DanteR along with the R programming environment. For Linux and Mac OS X, users must install R and then follow instructions on the DanteR website for package installation. CONTACT: [email protected].