@string{PNAS =   {Proc Natl Acad Sci U S A}}

@Article{Ritchie:NAR:2015,
    author = {M. E. Ritchie and B. Phipson and D. Wu and Y. Hu and C. W. Law and W. Shi and G. K. Smyth},
    title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
    journal = {Nucleic Acids Res},
    year = {2015},
    volume = {43},
    number = {7},
    pages = {e47},
  }

@Article{Robinson:Bioinformatics:2010,
    author = {M. D. Robinson and D. J. McCarthy and G. K. Smyth},
    title = {{edgeR}: a {Bioconductor} package for differential expression
  analysis of digital gene expression data.},
    journal = {Bioinformatics},
    year = {2010},
    volume = {26},
    pages = {139-140},
  }

@Article{Liao:NAR:2013,
    title = {The {S}ubread aligner: fast, accurate and scalable read mapping by seed-and-vote},
    author = {Y. Liao and G. K. Smyth and W. Shi},
    journal = {Nucleic Acids Res},
    year = {2013},
    volume = {41},
    issue = {10},
    pages = {e108},
  }

@Article{Huber:NatureMethods:2015,
    author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. {MacDonald} and V. Obenchain and A. K. {Ole\'s} and A. K. and H. {Pag\`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and  M. Morgan},
    title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
    journal = {Nature Methods},
    year = {2015},
    volume = {12},
    number = {2},
    pages = {115--121},
    url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
  }

@Article{Liao:Bioinformatics:2014,
  title={{featureCounts:} an efficient general-purpose program for assigning sequence reads to genomic features.},
  author={Y. Liao and G. K. Smyth and W. Shi},
  journal={Bioinformatics},
  volume={30},
  number={7},
  pages={923-30},
  year={2014}
}

@Article{Law:GenomeBiol:2014,
Author = 	 {C. W. Law and Y. Chen and W. Shi and G. K. Smyth},
Title = 	 {{Voom:} precision weights unlock linear model analysis tools for {RNA-seq} read counts.},
Journal = 	 {Genome Biology},
Year = 	 {2014},
Volume = 	 {15},
Number =  {},
Pages = 	 {R29}
}

@Article{RobinsonOshlack:GenomeBiol:2010,
Author = 	 {M. D. Robinson and A. Oshlack},
Title = 	 {A scaling normalization method for differential expression analysis of {RNA-seq data}},
Journal = 	 {Genome Biology},
Year = 	 {2010},
Volume = 	 {11},
Number =  {},
Pages = 	 {R25}
}

% Empirical Bayes
@Article{Smyth:SAGMB:2004,
Author = 	 {G. K. Smyth},
Title = 	 {Linear models and empirical {B}ayes methods for assessing differential expression in microarray experiments},
Journal = 	 {Stat Appl Genet Mol Biol},
Year = 	 {2004},
Volume = 	 {3},
Number = 	 {1},
Pages = 	 {Article 3}
}

@Article{Wu:NAR:2012,
author = {D. Wu and G. K. Smyth},
issn = {1362-4962},
journal = {Nucleic Acids Res},
month = sep,
number = {17},
pages = {e133},
title = {{Camera: a competitive gene set test accounting for inter-gene correlation.}},
volume = {40},
year = {2012}
}

@article{Wu:Bioinf:2010,
author = {D. Wu and E. Lim and F. Vaillant and M. L. Asselin-Labat and J. E. Visvader and G. K. Smyth},
title = {{ROAST: rotation gene set tests for complex microarray experiments}},
journal = {Bioinformatics},
year = {2010},
volume = {26},
number = {17},
pages = {2176--82}
}

@Manual{R,
         author = {{R Development Core Team}},
	  title   = {R: A language and environment for statistical computing}, 
	    organization  = {R Foundation for Statistical Computing}, 
	    address = {Vienna},
	    year    = {2016},
	    url = {http://www.R-project.org}
}

@Article{Liu:NAR:2015,
    title = {{Why weight? Combining voom with estimates of sample quality improves power in RNA-seq analyses.}},
    author = {R. Liu and A. Z. Holik and S. Su and N. Jansz and K. Chen and H. S. Leong and M. E. Blewitt and M. L. {Asselin-Labat} and G. K. Smyth and M. E. Ritchie},
    year = {2015},
    journal = {Nucleic Acids Res},
    volume = {43},
    pages = {e97},
}

@Manual{Glimma:2016,
    title = {{Glimma: Interactive HTML graphics for RNA-seq data}},
    author = {S. Su and M. E. Ritchie},
    year = {2016},
    note = {R package version 1.1.1},
    url = {https://bioconductor.org/packages/devel/bioc/html/Glimma.html}
}

@Manual{orgMm:2016,
    title = {{Mus.musculus: Annotation package for the Mus.musculus object}},
    author = {{Bioconductor Core Team}},
    year = {2016},
    note = {R package version 1.3.1},
    url = {https://bioconductor.org/packages/release/data/annotation/html/Mus.musculus.html}
}

@Manual{orgHs:2016,
    title = {{Homo.sapiens: Annotation package for the Homo.sapiens object}},
    author = {{Bioconductor Core Team}},
    year = {2016},
    note = {R package version 1.3.1},
    url = {https://bioconductor.org/packages/release/data/annotation/html/Homo.sapiens.html}
}

@Article{Durinck:NatureProtocols:2009,
    title = {{Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt}},
    author = {S. Durinck and P. Spellman and E. Birney and W. Huber},
    year = {2009},
    journal = {Nature Protocols},
    volume = {4},
    pages = {1184--91},
}

@Article{Durinck:Bioinf:2005,
    title = {{BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis}},
    author = {S. Durinck and Y. Moreau and A. Kasprzyk and S. Davis and B. {De Moor} and A. Brazma and W. Huber},
    year = {2005},
    journal = {Bioinformatics},
    volume = {21},
    pages = {3439--40},
}

@article{Sheridan:BMCCancer:2015,
author = {J. M. Sheridan and M. E. Ritchie and S. A. Best and K. Jiang and T. J. Beck and F. Vaillant and K. Liu and R. A. Dickins and G. K. Smyth and G. J. Lindeman and J. E. Visvader},
journal = {BMC Cancer},
number = {1},
pages = {221},
publisher = {BioMed Central},
title = {{A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1}},
volume = {15},
year = {2015}
}

@article{McCarthy:Bioinf:2009,
author = {D. J. McCarthy and G. K. Smyth},
journal = {Bioinformatics},
number = {},
pages = {765--71},
title = {{Testing significance relative to a fold-change threshold is a TREAT}},
volume = {25},
year = {2009}
}

@article{Lim:BreastCancerRes:2010,
author = {E. Lim and D. Wu and B. Pal and T. Bouras and M. L. {Asselin-Labat} and F. Vaillant and H. Yagita and G. J. Lindeman and G. K. Smyth and J. E. Visvader},
journal = {Breast Cancer Research},
number = {2},
pages = {R21},
title = {{Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways.}},
volume = {12},
year = {2010}
}


@article{Subramanianetal:PNAS:2005,
   Author = {Subramanian, A. and Tamayo, P. and Mootha, V. K. and Mukherjee, S. and Ebert, B. L. and Gillette, M. A. and Paulovich, A. and Pomeroy, S. L. and Golub, T. R. and Lander, E. S. and Mesirov, J. P.},
   Title = {Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles},
   Journal = PNAS,
   Volume = {102},
   Number = {43},
   Pages = {15545-50},
   Year = {2005}
}

@article{Liu:GenomicsData:2016,
    title = {Transcriptional profiling of the epigenetic regulator {S}mchd1.},
    author = {R. Liu and K. Chen and N. Jansz and M. E. Blewitt and M. E. Ritchie},
    year = {2016},
    journal = {Genomics Data},
    volume = {7},
    month = {},
    pages = {144-7}
}

@Manual{knitr2016,
    title = {knitr: A General-Purpose Package for Dynamic Report
      Generation in R},
    author = {Y. Xie},
    year = {2016},
    note = {R package version 1.12.3},
    url = {http://yihui.name/knitr/},
}

@Book{knitr2015,
    title = {Dynamic Documents with {R} and knitr},
    author = {Y. Xie},
    publisher = {Chapman and Hall/CRC},
    address = {Boca Raton, Florida},
    year = {2015},
    edition = {2nd},
    note = {ISBN 978-1498716963},
    url = {http://yihui.name/knitr/},
}

@InCollection{knitr2014,
    booktitle = {Implementing Reproducible Computational Research},
    editor = {V. Stodden and F. Leisch and R. D. Peng},
    title = {knitr: A Comprehensive Tool for Reproducible Research in
      {R}},
    author = {Y. Xie},
    publisher = {Chapman and Hall/CRC},
    year = {2014},
    note = {ISBN 978-1466561595},
    url = {http://www.crcpress.com/product/isbn/9781466561595},
}

 @Manual{gplots,
    title = {gplots: Various R Programming Tools for Plotting Data},
    author = {G. R. Warnes and B. Bolker and L. Bonebakker and R. Gentleman and W. Huber and A. Liaw and T. Lumley and M. Maechler and A. Magnusson and S. Moeller and M. Schwartz and B. Venables},
    year = {2016},
    note = {R package version 3.0.1},
    url = {https://CRAN.R-project.org/package=gplots},
  }