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Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer
Deena M A Gendoo1, Natchar Ratanasirigulchai2, Markus S Schröder3
1Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Unlabelled:
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. http://www.bioconductor.org/packages/devel/bioc/html/genefu.html Source code is also available on Github https://github.com/bhklab/genefu
Contact:
bhaibeka@uhnresearch.ca
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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