title: Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
abstract: 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.
  
  
  
  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
  
  
  
  bhaibeka@uhnresearch.ca
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Deena M A
authors.initials: DM
authors.lastname: Gendoo
authors.affiliation: Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and.
authors.forename: Natchar
authors.initials: N
authors.lastname: Ratanasirigulchai
authors.affiliation: UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, UK.
authors.forename: Markus S
authors.initials: MS
authors.lastname: Schröder
authors.affiliation: Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.
authors.forename: Laia
authors.initials: L
authors.lastname: Paré
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
authors.affiliation: Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain, Translational Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain and Department of Medical Oncology, Hospital Clínic of Barcelona, 08036 Barcelona, Spain.
authors.forename: Aleix
authors.initials: A
authors.lastname: Prat
authors.affiliation: Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics*; D005260:Female; D006801:Humans; D011381:Programming Languages; D012984:Software; D059467:Transcriptome