index.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},
}

@Manual{colladotorres2015regionreport,
  title = {regionReport: Generate HTML reports for exploring a set of regions},
  author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
  year = {2015},
  url = {http://www.bioconductor.org/packages/release/bioc/html/regionReport.html},
  note = {https://github.com/leekgroup/regionReport - R package version 1.4.1},
}

@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{love2014moderated,
  title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author = {Michael I Love and Wolfgang Huber and Simon Anders},
  year = {2014},
  journal = {Genome Biology},
  doi = {10.1186/s13059-014-0550-8},
  volume = {15},
  issue = {12},
  pages = {550},
}

@Article{zhou2014robustly,
  title = {Robustly detecting differential expression in RNA sequencing data using observation weights},
  author = {Xiaobei Zhou and Helen Lindsay and Mark D Robinson},
  journal = {Nucleic Acids Research},
  volume = {42},
  pages = {e91},
  year = {2014},
}

@Manual{morganbiocstyle,
  title = {BiocStyle: Standard styles for vignettes and other Bioconductor documents},
  author = {Martin Morgan and Andrzej Ole{\a's} and Wolfgang Huber},
  note = {R package version 1.8.0},
  url = {https://github.com/Bioconductor/BiocStyle},
}

@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 0.9.2},
  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{zhou2011,
  author = {{Zhou} and {Zhifeng} and {Yuan} and {Qiaoping} and {Mash} and Deborah C and {Goldman} and {David}},
  title = {Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2011},
  volume = {108},
  number = {16},
  pages = {6626-6631},
}

@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},
}

@Article{stringtie,
  author = { Mihaela Pertea and Geo M. Pertea and Corina M. Antonescu and Tsung-Cheng Chang and Joshua T. Mendell and Steven L. Salzberg},
  journal = {Nature Biotechnology},
  year = {2015},
  title = {StringTie enables improved reconstruction of a transcriptome from RNA-seq reads},
}

@Article{hisat,
  author = {Daehwan Kim and Ben Langmead and Steven L Salzberg},
  journal = {Nature Methods},
  year = {2015},
  title = {HISAT: a fast spliced aligner with low memory requirements},
}

@Article{ballgown,
  author = {Alyssa C. Frazee and Geo Pertea and Andrew E. Jaffe and Ben Langmead and Steven L. Salzberg and Jeffrey T. Leek},
  journal = {Nature Biotechnology},
  year = {2015},
  title = {Ballgown bridges the gap between transcriptome assembly and expression analysis},
}