timing.bib

@Manual{boettiger2015knitcitations,
  title = {knitcitations: Citations for 'Knitr' Markdown Files},
  author = {Carl Boettiger},
  year = {2015},
  note = {R package version 1.0.7},
  url = {http://CRAN.R-project.org/package=knitcitations},
}

@Article{colladotorres2015derfinder,
  title = {derfinder: Software for annotation-agnostic RNA-seq differential expression analysis},
  author = {Leonardo Collado-Torres and Alyssa C. Frazee and Michael I. Love and Rafael A. Irizarry and Andrew E. Jaffe and Jeffrey T. Leek},
  year = {2015},
  journal = {bioRxiv},
  doi = {10.1101/015370},
  url = {http://www.biorxiv.org/content/early/2015/02/19/015370.abstract},
}

@Article{frazee2014differential,
  title = {Differential expression analysis of RNA-seq data at single-base resolution},
  author = {Alyssa C. Frazee and Sarven Sabunciyan and Kasper D. Hansen and Rafael A. Irizarry and Jeffrey T. Leek},
  year = {2014},
  journal = {Biostatistics},
  volume = {15 (3)},
  pages = {413-426},
  doi = {10.1093/biostatistics/kxt053},
  url = {http://biostatistics.oxfordjournals.org/content/15/3/413.long},
}

@Article{lawrence2013software,
  title = {Software for Computing and Annotating Genomic Ranges},
  author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
  year = {2013},
  journal = {{PLoS} Computational Biology},
  volume = {9},
  issue = {8},
  doi = {10.1371/journal.pcbi.1003118},
  url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
}

@Article{anders2010differential,
  title = {Differential expression analysis for sequence count data},
  author = {Simon Anders and Wolfgang Huber},
  year = {2010},
  journal = {Genome Biology},
  volume = {11},
  pages = {R106},
  doi = {10.1186/gb-2010-11-10-r106},
  url = {http://genomebiology.com/2010/11/10/R106/},
}

@Manual{xie2015wrapper,
  title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
  author = {Yihui Xie},
  year = {2015},
  note = {R package version 0.1},
  url = {http://CRAN.R-project.org/package=DT},
}

@Book{wickham2009ggplot2,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2009},
  isbn = {978-0-387-98140-6},
  url = {http://had.co.nz/ggplot2/book},
}

@Manual{allaire2016rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Joe Cheng and Yihui Xie and Jonathan McPherson and Winston Chang and Jeff Allen and Hadley Wickham and Aron Atkins and Rob Hyndman},
  year = {2016},
  note = {R package version 0.9.5},
  url = {http://CRAN.R-project.org/package=rmarkdown},
}

@InCollection{xie2014knitr,
  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 = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Manual{eff,
  title = {Efficiency analysis of Sun Grid Engine batch jobs},
  author = {Alyssa Frazee},
  year = {2014},
  url = {http://dx.doi.org/10.6084/m9.figshare.878000},
}

@Article{rail,
  author = {Abhinav Nellore and Leonardo Collado-Torres and Andrew E. Jaffe and Jos{\a'e} Alquicira-Hern{\a'a}ndez and Jacob Pritt and James Morton and Jeffrey T. Leek and Ben Langmead},
  journal = {bioRxiv},
  year = {2015},
  title = {Rail-RNA: {Scalable} analysis of {RNA}-seq splicing and coverage},
}