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Summary: Breast cancer is one of the most frequent cancers among women. Extensive studies into themolecular heterogeneity of breast cancer have produced a plethora ofmolecular subtype classification and prognosis prediction algorithms, as well as numerous gene expression signatures. However, reimplementation of these algorithms is a tedious but important task to enable comparison of existing signatures and classification models between each other and with new models. Here, we present the genefu R/Bioconductor package, a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. Availability and implementation: The genefu package is available from Bioconductor. http://www. bioconductor.org/packages/devel/bioc/html/genefu.html. Source code is also available on Github https://github.com/bhklab/genefu. [ABSTRACT FROM AUTHOR]