@Article{Anders:2010:GB,
  url =		 {http://genomebiology.com/2010/11/10/R106},
  author =	 {Simon Anders and Wolfgang Huber},
  Title =	 {{D}ifferential expression analysis for sequence
                  count data},
  Journal =	 {Genome Biology},
  Year =	 2010,
  Volume =	 11,
  Pages =	 {R106},
}

@article{DEXSeqPaper,
  author =	 {Simon Anders and Alejandro Reyes and Wolfgang Huber},
  title =	 {Detecting differential usage of exons from {RNA-seq}
                  data},
  year =	 2012,
  journal =	 {Genome Research},
  Volume =	 22,
  Pages =	 "2008",
  doi =		 {10.1101/gr.133744.111},
}

@article{Brooks2010,
  author =	 {Angela N. Brooks and Li Yang and Michael O. Duff and Kasper D. Hansen and
   Jung W. Park and Sandrine Dudoit and Steven E. Brenner and Brenton R. Graveley},
  doi =		 {10.1101/gr.108662.110},
  issn =	 {1088},
  journal =	 {Genome Research},
  volume = {21},
  pages =	 {193--202},
  title =	 {{Conservation of an RNA regulatory map between
                  Drosophila and mammals}},
  url =
                  {http://genome.cshlp.org/cgi/doi/10.1101/gr.108662.110},
  year =	 2011
}

@article{edgeR,
  author =	 {Robinson, Mark D. and Smyth, Gordon K.},
  title =	 {Moderated statistical tests for assessing
                  differences in tag abundance},
  journal =	 {Bioinformatics},
  volume =	 23,
  pages =	 {2881},
  doi =		 {10.1093/bioinformatics/btm453},
  year =	 2007,
  URL =          {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881},
  eprint =       {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf}
}

@article{edgeR_GLM,
  author = {McCarthy, Davis J. and Chen, Yunshun and Smyth, Gordon K.},
  year = {2012},
  title = {Differential expression analysis of multifactor {RNA-Seq} experiments with respect to biological variation},
  journal = {Nucleic Acids Research},
  volume = {40}, 
  pages = {4288-4297}
}  


@misc{pasillaVignette,
  title = {Data preprocessing and creation of the data objects {pasillaGenes} and {pasillaExons}},
  author = {Alejandro Reyes},
  year = {2013},
  howpublished = {Vignette to Bioconductor data package \emph{pasilla}, \url{http://bioconductor.org/packages/release/data/experiment/html/pasilla.html}}
}

@article{DEProt,
   title = {Count-based differential expression analysis of {RNA} sequencing data using {R} and {Bioconductor}},
   author = {Simon Anders and Davis J. McCarthy and Yunshen Chen and Michal Okoniewski and Gordon K. Smyth and Wolfgang Huber and Mark D. Robinson},
   year = {2013},
   journal = {Nature Protocols},
   volume = {8},
   pages = {1765},
   doi = {10.1038/nprot.2013.099}
}

@misc{parathyroidSEVignette,
  title = {{SummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012}},
  author = {Michael Love},
  year = {2013},
  howpublished = {Vignette to Bioconductor data package \emph{parathyroidSE}, \url{http://bioconductor.org/packages/release/data/experiment/html/parathyroidSE.html}}
}

@article{parathyroidPaper,
author = {Haglund, Felix and Ma, Ran and Huss, Mikael and Sulaiman, Luqman and Lu, Ming and Nilsson, Inga-Lena and H\"o\"og, Anders and Juhlin, C. Christofer and Hartman, Johan and Larsson, Catharina}, 
title = {Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas},
volume = {97}, 
number = {12}, 
year = {2012}, 
doi = {10.1210/jc.2012-2484}, 
URL = {http://jcem.endojournals.org/content/97/12/4631.abstract}, 
eprint = {http://jcem.endojournals.org/content/97/12/4631.full.pdf+html}, 
journal = {Journal of Clinical Endocrinology \& Metabolism} 
}

@article{TopHat2,
AUTHOR = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven},
TITLE = {TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions},
JOURNAL = {Genome Biology},
VOLUME = {14},
YEAR = {2013},
NUMBER = {4},
PAGES = {R36},
URL = {http://genomebiology.com/2013/14/4/R36},
DOI = {10.1186/gb-2013-14-4-r36},
}

@article{GSNAP,
author = {Wu, Thomas D. and Nacu, Serban}, 
title = {Fast and {SNP}-tolerant detection of complex variants and splicing in short reads},
volume = {26}, 
number = {7}, 
pages = {873-881}, 
year = {2010}, 
doi = {10.1093/bioinformatics/btq057}, 
URL = {http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/26/7/873.full.pdf+html}, 
journal = {Bioinformatics} 
}

@article{STAR,
author = {Dobin, Alexander and Davis, Carrie A. and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R.}, 
title = {{STAR}: ultrafast universal {RNA-seq} aligner},
volume = {29}, 
number = {1}, 
pages = {15-21}, 
year = {2013}, 
doi = {10.1093/bioinformatics/bts635}, 
URL = {http://bioinformatics.oxfordjournals.org/content/29/1/15.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/29/1/15.full.pdf+html}, 
journal = {Bioinformatics} 
}

@misc{ExpressionSet,
  title = {An Introduction to {Bioconductor's} {ExpressionSet} Class},
  author = {Seth Falcon and Martin Morgan and Robert Gentleman},
  year = {2007},
  howpublished = {Vignette, provided with Bioconductor package \emph{Biobase}, \url{http://http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf}}
}

@article{hwriter,
    title={The hwriter Package},
    author={Gregoire Pau and Wolfgang Huber},
    journal={The R Journal},
    volume={1},
    issue={1},
    pages={22},
    url={http://journal.r-project.org/archive/2009-1/RJournal_2009-1_Pau+Huber.pdf},
    year=2009
}

@article{deseq2,
    author = {Michael I Love and Wolfgang Huber and Simon Anders},
    title = {{Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2}},
    year = {2014},
    doi = {10.1101/002832},
    URL = {http://biorxiv.org/content/early/2014/02/19/002832},
    eprint = {http://biorxiv.org/content/early/2014/02/19/002832.full.pdf},
    journal = {bioRxiv}
}


@Article{soneson2015,
author="Soneson, Charlotte
and Matthes, Katarina L.
and Nowicka, Malgorzata
and Law, Charity W.
and Robinson, Mark D.",
title="Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage",
journal="Genome Biology",
year="2016",
volume="17",
number="1",
pages="1--15",
issn="1474-760X",
doi="10.1186/s13059-015-0862-3",
url="http://dx.doi.org/10.1186/s13059-015-0862-3"
}

