@book{R:Kabacoff:2010,
  author = {Rob Kabacoff},
  title = {{R} in Action},
  publisher = {Manning},
  url = {http://www.manning.com/kabacoff},
  year = 2010
}
                  
@Book{Matloff2011,
  Author = 	 {Matloff, N.},
  title = 	 {The Art of {R} Programming},
  publisher = 	 {No Starch Pess},
  year = 	 2011,
  pages  = 373
}

@book{R:Dalgaard:2008,
  author = {Peter Dalgaard},
  title = {Introductory Statistics with {R}},
  edition = {2nd},
  year = 2008,
  publisher = {Springer},
  isbn = {978-0-387-79053-4},
  pages = 380,
  url = {http://www.biostat.ku.dk/~pd/ISwR.html},
  publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-79053-4},
  orderinfo = {springer.txt},
  abstract = {This book provides an elementary-level introduction to
                  R, targeting both non-statistician scientists in
                  various fields and students of statistics. The main
                  mode of presentation is via code examples with liberal
                  commenting of the code and the output, from the
                  computational as well as the statistical viewpoint. A
                  supplementary R package can be downloaded and contains
                  the data sets.  The statistical methodology includes
                  statistical standard distributions, one- and
                  two-sample tests with continuous data, regression
                  analysis, one- and two-way analysis of variance,
                  regression analysis, analysis of tabular data, and
                  sample size calculations. In addition, the last six
                  chapters contain introductions to multiple linear
                  regression analysis, linear models in general,
                  logistic regression, survival analysis, Poisson
                  regression, and nonlinear regression.}
}

@book{hahne2008bioconductor,
  title={Bioconductor case studies},
  author={Hahne, F. and Huber, W. and Gentleman, R. and Falcon, S.},
  year={2008},
  publisher={Springer}
}
                  
@book{meys2012r,
  title={R For Dummies},
  author={Meys, J. and de Vries, A.},
  year={2012},
  publisher={For Dummies}
}
                  
@book{R:Gentleman:2008b,
  author = {Robert Gentleman},
  title = {{R} Programming for Bioinformatics},
  publisher = {Chapman \& Hall/CRC},
  year = 2008,
  series = {Computer Science \& Data Analysis},
  address = {Boca Raton, FL},
  isbn = {978-1-420-06367-7},
  url = {http://www.bioconductor.org/pub/RBioinf/},
  publisherurl = {http://crcpress.com/shopping_cart/products/product_detail.asp?sku=C6367},
  abstract = {Thanks to its data handling and modeling capabilities
                  and its flexibility, R is becoming the most widely
                  used software in bioinformatics.  R Programming for
                  Bioinformatics builds the programming skills needed to
                  use R for solving bioinformatics and computational
                  biology problems.  Drawing on the author's experiences
                  as an R expert, the book begins with coverage on the
                  general properties of the R language, several unique
                  programming aspects of R, and object-oriented
                  programming in R. It presents methods for data input
                  and output as well as database interactions. The
                  author also examines different facets of string
                  handling and manipulations, discusses the interfacing
                  of R with other languages, and describes how to write
                  software packages. He concludes with a discussion on
                  the debugging and profiling of R code.},
  orderinfo = {crcpress.txt}
}
            
@book{R:Chambers:2008,
  author = {John M. Chambers},
  title = {Software for Data Analysis: Programming with {R}},
  publisher = {Springer},
  year = 2008,
  address = {New York},
  isbn = {978-0-387-75935-7},
  url = {http://stat.stanford.edu/~jmc4/Rbook/},
  publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-75935-7},
  abstract = {The R version of S4 and other R techniques.  This book
                  guides the reader in programming with R, from
                  interactive use and writing simple functions to the
                  design of R packages and intersystem interfaces.},
  orderinfo = {springer.txt}
}
                  
@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
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    organization = {R Foundation for Statistical Computing},
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    year = {2012},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
}

@Article{Bioc,
    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},
}

@TechReport{RInferno,
  author =       {Burns, P},
  title =        {The {R} Inferno},
  year =         {2011},
  url = {http://www.burns-stat.com/pages/Tutor/R_inferno.pdf}
}

@article{pasilla,
  author =	 {Brooks, A. N. and Yang, L. and Duff, M. O. and
                  Hansen, K. D. and Park, J. W. and Dudoit, S. and
                  Brenner, S. E. and Graveley, B. R.},
  doi =		 {10.1101/gr.108662.110},
  issn =	 {1088-9051},
  journal =	 {Genome Research},
  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{anders2010differential,
  title={Differential expression analysis for sequence count data},
  author={Anders, S. and Huber, W.},
  journal={Genome Biol},
  volume={11},
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  pages={R106},
  year={2010}
}

@Manual{Rparallel,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2013},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
  }

@article{SchmidbergerEtAl:2009,
  author =	"Markus  Schmidberger and Martin Morgan and Dirk Eddelbuettel and Hao Yu and Luke Tierney and Ulrich Mansmann",
  title =	"State of the Art in Parallel Computing with R",
  journal =	"Journal of Statistical Software",
  volume =	"31",
  number =	"1",
  pages =	"1--27",
  day =  	"4",
  month =	"8",
  year = 	"2009",
  CODEN =	"JSSOBK",
  ISSN = 	"1548-7660",
  bibdate =	"2009-06-02",
  URL =  	"http://www.jstatsoft.org/v31/i01",
  accepted =	"2009-06-02",
  acknowledgement = "",
  keywords =	"",
  submitted =	"2008-12-29",
}

@article{rothberg2008,
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  pages={1117--1124},
  year={2008},
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@article{bentley2008,
  title={Accurate whole human genome sequencing using reversible terminator chemistry},
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@Article{pmid20080505,
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@Article{pmid19261174,
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@article{shendure2008next,
  title={Next-generation DNA sequencing},
  author={Shendure, J. and Ji, H.},
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% 19736561 
@Article{pmid19736561,
   Author="Park, P. J. ",
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@article{ross2012differential,
  title={Differential oestrogen receptor binding is associated with clinical outcome in breast cancer},
  author={Ross-Innes, C.S. and Stark, R. and Teschendorff, A.E. and Holmes, K.A. and Ali, H.R. and Dunning, M.J. and Brown, G.D. and Gojis, O. and Ellis, I.O. and Green, A.R. and others},
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@article{marioni2008rna,
  title={RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays},
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@article{mortazavi2008mapping,
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@article{hansen2010biases,
  title={Biases in Illumina transcriptome sequencing caused by random hexamer priming},
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@article{bullard2010evaluation,
  title={Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments},
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    number = {2},
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    title = {A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data},
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  @book{wickham2009ggplot2,
  title={ggplot2: elegant graphics for data analysis},
  author={Wickham, Hadley},
  year={2009},
  publisher={Springer Publishing Company, Incorporated}
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@book{sarkar2008lattice,
  title={Lattice: multivariate data visualization with R},
  author={Sarkar, Deepayan},
  year={2008},
  publisher={Springer}
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@book{murrell2005r,
  title={R graphics},
  author={Murrell, Paul},
  year={2005},
  publisher={Chapman \& Hall/CRC}
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@book{chang2012r,
  title={R Graphics Cookbook},
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  year={2012},
  publisher={O'Reilly Media, Incorporated}
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  pages={1353--1358},
  year={2012},
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@article{zarnack2013direct,
  title={Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of< i> Alu</i> Elements},
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  volume={152},
  number={3},
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@article{liao2013featurecounts,
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  year={2013}
}
@article{huang2013highly,
  title={Highly Recurrent TERT Promoter Mutations in Human Melanoma},
  author={Huang, Franklin W and Hodis, Eran and Xu, Mary Jue and Kryukov, Gregory V and Chin, Lynda and Garraway, Levi A},
  journal={Science},
  volume={339},
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  year={2013},
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@article{mclaren2010deriving,
  title={Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor},
  author={McLaren, William and Pritchard, Bethan and Rios, Daniel and Chen, Yuan and Flicek, Paul and Cunningham, Fiona},
  journal={Bioinformatics},
  volume={26},
  number={16},
  pages={2069--2070},
  year={2010},
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}