SOFTWARE

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The seventyGeneData R package contains the gene expression data for the van't Veer and Van de Vijver breast cancer cohorts. To install this package:

• Use an up-to-date version of R and Bioconductor, start an R session, and then execute the following:

   source("http://www.bioconductor.org/biocLite.R") 
  biocLite("seventyGeneData")
  

• To obtain the breastCancerNKI, which is suggested by our package, you can run the execute the following commands:

  source("http://www.bioconductor.org/biocLite.R")
  biocLite("breastCancerNKI")

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The mammaPrintData R package contains the gene expression data for the Glas and Buyse breast cancer cohorts. To install this package:

• Use an up-to-date version of R and Bioconductor, start an R session, and then execute the following:

   source("http://www.bioconductor.org/biocLite.R")
  biocLite("mammaPrintData")

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The switchBox R package contains functions to develop simple K-Top-Scoring-Pair classifiers for binary data. The package was written in collaboration with Bahman Afsari and Wikum Dinalankara. To install it:

• Use an up-to-date version of R and Bioconductor, start an R session, and then execute the following:

   source("http://www.bioconductor.org/biocLite.R")
  biocLite("switchBox")

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The matchBox R package contains functions to compute and plot Correspondence-At-the_Top curves. To install it:

• Use an up-to-date version of R and Bioconductor, start an R session, and then execute the following:

    source("http://www.bioconductor.org/biocLite.R")
  biocLite("matchBox")

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 The RTopper R-Bioconductor package is designed to perform Gene Set Analysis across multiple genomic platforms. To install it from Bioconductor you need:

• Use an up-to-date version of R and Bioconductor, start an R session, and then execute the following:

  source("http://www.bioconductor.org/biocLite.R")
  biocLite("RTopper")

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