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@INCOLLECTION{chen2014edgerchapter,
  title = {Differential expression analysis of complex {RNA}-seq experiments using {edgeR}},
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@ARTICLE{chen2016quasiworkflow,
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@article{chen2025edger4,
  title={{edgeR} v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets},
  author={Chen, Yunshun and Chen, Lizhong and Lun, Aaron T L and Baldoni, Pedro L and Smyth, Gordon K},
  journal={Nucleic Acids Research},
  volume={53},
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  year={2025},
  publisher={Oxford University Press}
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@article{ching2014power,
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@BOOK{dunn2018glms,
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@ARTICLE{fu2015egfmcl1,
  author = {N. Y. Fu and A. Rios and B. Pal and R. Soetanto and A. T. L. Lun and K. Liu and T. Beck and S. Best and F. Vaillant and P. Bouillet and A. Strasser and T. Preiss and G. K. Smyth and G. Lindeman and and J. Visvader},
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@article{germain2016rnaonthebench,
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@ARTICLE{law2014voom,
  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},
  pages = {R29},
  doi = {10.1186/gb-2014-15-2-r29}
}

@ARTICLE{liao2013subread,
  author = {Y. Liao and G. K. Smyth and W. Shi},
  title = {The {Subread} aligner: fast, accurate and scalable read mapping by seed-and-vote},
  journal = {Nucleic Acids Research},
  year = {2013},
  volume = {41},
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}

@ARTICLE{liao2014featurecounts,
  author = {Y. Liao and G. K. Smyth and W. Shi},
  title = {{featureCounts}: an efficient general-purpose read summarization program},
  journal = {Bioinformatics},
  year = {2014},
  volume = {30},
  number = {7},
  pages = {923-930},
  doi = {10.1093/bioinformatics/btt656}
}

@ARTICLE{lim2010transcriptome,
  author = {Lim, E. and Wu, D. and Pal, B. and Bouras, T. and Asselin-Labat, M.L. and Vaillant, F. and Yagita, H. and Lindeman, G.J. and Smyth, G.K. and Visvader, J.E.},
  title = {Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways},
  journal = {Breast Cancer Research},
  year = {2010},
  volume = {12},
  pages = {R21},
}

@ARTICLE{love2014deseq2,
  title = {Moderated estimation of fold change and dispersion for {RNA-seq} data with {DESeq2}},
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  journal = {Genome Biology},
  year = {2014},
  volume = {15},
  number = {12},
  pages = {550}
}

@ARTICLE{lun2014denovo,
  title = {De novo detection of differentially bound regions for {ChIP-seq} data using peaks and windows: controlling error rates correctly},
  author = {A. T. L. Lun and G. K. Smyth},
  journal = {Nucleic Acids Research},
  year = {2014},
  volume = {42},
  number = {11},
  pages = {e95},
  doi = {10.1093/nar/gku351}
}

@ARTICLE{lun2015diffhic,
  author = {A. T. L. Lun and G. K. Smyth},
  title = {{diffHic}: a Bioconductor package to detect differential genomic interactions in {Hi-C} data},
  journal = {BMC Bioinformatics},
  year = {2015},
  volume = {16},
  pages = {258},
  doi = {10.1186/s12859-015-0683-0}
}

@ARTICLE{lun2016delicious,
  title = {It's {DE}-licious: a recipe for differential expression analyses of {RNA}-seq experiments using quasi-likelihood methods in {edgeR}},
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  year = {2016},
  volume = {1418},
  pages = {391-416},
  doi = {10.1007/978-1-4939-3578-9_19}
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@article{lun2016pooling,
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  pages = {75},
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@ARTICLE{lund2012quasiseq,
  author = {Lund, S. P. and Nettleton, D. and McCarthy, D. J. and Smyth, G. K.},
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@ARTICLE{mccarthy2009treat,
  author = {D. J. McCarthy and G. K. Smyth},
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  pages = {765--771},
  number = {6},
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@ARTICLE{mccarthy2012edgerglm,
  author = {D. J. McCarthy and Y. Chen and G. K. Smyth},
  title = {Differential expression analysis of multifactor {RNA-Seq} experiments with respect to biological variation},
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@ARTICLE{phipson2016robust,
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  year = {2016},
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@article{rajkumar2015experimental,
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@ARTICLE{ritchie2015limma,
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@ARTICLE{robinson2008smallsample,
  author = {M. D. Robinson and G. K. Smyth},
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  pages = {321--332},
  number = {2},
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@ARTICLE{robinson2007moderated,
  author = {M. D. Robinson and G. K. Smyth},
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  title = {A scaling normalization method for differential expression analysis of {RNA-seq} data},
  volume = {11},
  year = {2010},
}

@ARTICLE{robinson2010edger,
  author = {Robinson, M. D. and McCarthy, D. J. and Smyth, G. K.},
  title = {{edgeR}: a {B}ioconductor package for differential expression analysis of digital gene expression data},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {139--140},
  number = {1},
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@ARTICLE{subramanian2005gsea,
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@ARTICLE{wu2010roast,
  author = {Wu, D. and Lim, E. and Vaillant, F. and Asselin-Labat, M. L. and Visvader, J. E. and Smyth, G. K.},
  title = {{ROAST}: rotation gene set tests for complex microarray experiments},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {2176--2182},
  number = {17},
  doi = {10.1093/bioinformatics/btq401}
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@article{wu2013mirna,
  title={The use of {miRNA} microarrays for the analysis of cancer samples with global {miRNA} decrease},
  author={Wu, Di and Hu, Yifang and Tong, Stephen and Williams, Bryan RG and Smyth, Gordon K and Gantier, Michael P},
  journal={RNA},
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  year={2013},
}
