Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer

Bioinformatics. 2016 Apr 1;32(7):1097-9. doi: 10.1093/bioinformatics/btv693. Epub 2015 Nov 24.


Breast cancer is one of the most frequent cancers among women. Extensive studies into the molecular heterogeneity of breast cancer have produced a plethora of molecular 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. Source code is also available on Github


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms*
  • Breast Neoplasms / genetics*
  • Female
  • Humans
  • Programming Languages
  • Software
  • Transcriptome*