@Article{biomaRt1,
  title = {Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt},
  author = {Steffen Durinck and Paul T. Spellman and Ewan Birney and Wolfgang Huber},
  journal = {Nature Protocols},
  year = {2009},
  volume = {4},
  pages = {1184--1191},
}

@Article{biomaRt2,
  title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis},
  author = {Steffen Durinck and Yves Moreau and Arek Kasprzyk and Sean Davis and Bart {De Moor} and Alvis Brazma and Wolfgang Huber},
  journal = {Bioinformatics},
  year = {2005},
  volume = {21},
  pages = {3439--3440},
}

@Article{GEOquery,
  author = {Sean Davis and Paul Meltzer},
  title = {GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor},
  journal = {Bioinformatics},
  year = {2007},
  volume = {14},
  pages = {1846--1847},
}

@Manual{knitcitations,
  title = {knitcitations: Citations for knitr markdown files},
  author = {Carl Boettiger},
  year = {2013},
  note = {R package version 0.5-0},
  url = {https://github.com/cboettig/knitcitations},
}

@Article{Biobase,
  author = {Robert C Gentleman and Vincent J. Carey and Douglas M. Bates and {others}},
  title = {Bioconductor: Open software development for computational biology and bioinformatics},
  journal = {Genome Biology},
  volume = {5},
  year = {2004},
  pages = {R80},
  url = {http://genomebiology.com/2004/5/10/R80},
}

@Manual{stats,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2013},
  url = {http://www.R-project.org/},
}

@Manual{knitr1,
  title = {knitr: A general-purpose package for dynamic report generation in R},
  author = {Alastair Andrew and Alex Zvoleff and Brian Diggs and Cassio Pereira and Hadley Wickham and Heewon Jeon and Jeff Arnold and Jeremy Stephens and Jim Hester and Joe Cheng and Jonathan Keane and J.J. Allaire and Johan Toloe and Kohske Takahashi and Michel Kuhlmann and Nacho Caballero and Nick Salkowski and Noam Ross and Ramnath Vaidyanathan and Richard Cotton and Romain Francois and Sietse Brouwer and Simon de Bernard and Taiyun Wei and Thibaut Lamadon and Tom Torsney-Weir and Trevor Davis and Weicheng Zhu and Wush Wu and Yihui Xie},
  year = {2013},
  note = {R package version 1.5},
  url = {http://yihui.name/knitr/},
}

@Book{knitr2,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2013},
  note = {ISBN 978-1482203530},
  url = {http://yihui.name/knitr/},
}

@InCollection{knitr3,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2013},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@InCollection{limma,
  title = {Limma: linear models for microarray data},
  author = {Gordon K Smyth},
  booktitle = {Bioinformatics and Computational Biology Solutions Using {R} and Bioconductor},
  editor = {R. Gentleman and V. Carey and S. Dudoit and R. Irizarry and W. Huber},
  publisher = {Springer},
  address = {New York},
  year = {2005},
  pages = {397--420},
}