@article{collado2017a,
	title = {Flexible expressed region analysis for {RNA}-seq with derfinder},
	volume = {45},
	issn = {0305-1048},
	doi = {10.1093/nar/gkw852},
	number = {2},
	urldate = {2017-04-13},
	journal = {Nucleic Acids Research},
	author = {Collado-Torres, Leonardo and Nellore, Abhinav and Frazee, Alyssa C. and Wilks, Christopher and Love, Michael I. and Langmead, Ben and Irizarry, Rafael A. and Leek, Jeffrey T. and Jaffe, Andrew E.},
	month = jan,
	year = {2017},
	pages = {e9--e9},
}

@article{collado2017b,
	title = {Reproducible {RNA}-seq analysis using recount2},
	volume = {35},
	issn = {1087-0156},
	doi = {10.1038/nbt.3838},
	language = {en},
	number = {4},
	journal = {Nature Biotechnology},
	author = {Collado-Torres, Leonardo and Nellore, Abhinav and Kammers, Kai and Ellis, Shannon E. and Taub, Margaret A. and Hansen, Kasper D. and Jaffe, Andrew E. and Langmead, Ben and Leek, Jeffrey T.},
	month = apr,
	year = {2017},
	pages = {319--321},
}

@Manual{biocWorkflow,
    title = {BiocWorkflowTools: Tools to aid the development of Bioconductor Workflow packages},
    author = {Mike Smith and Andrzej Ole{\'s}},
    year = {2017},
    note = {R package version 1.2.0},
}

@article{Law2016a,
author = {Law, Charity W and Alhamdoosh, Monther and Su, Shian and Smyth, Gordon K and Ritchie, Matthew E},
doi = {10.12688/f1000research.9005.2},
journal = {F1000Research},
number = {May},
pages = {1408},
pmid = {27441086},
title = {{RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.}},
volume = {5},
year = {2016}
}

@article{Love2016,
author = {Love, Michael I. and Anders, Simon and Kim, Vladislav and Huber, Wolfgang},
doi = {10.12688/f1000research.7035.2},
journal = {F1000Research},
number = {May},
pages = {1070},
pmid = {26674615},
title = {{RNA-Seq workflow: gene-level exploratory analysis and differential expression}},
volume = {4},
year = {2016}
}

@article{Chen2016,
author = {Chen, Yunshun and Lun, Aaron T L and Smyth, Gordon K},
doi = {10.12688/f1000research.8987.2},
issn = {2046-1402},
journal = {F1000Research},
number = {May},
pages = {1438},
pmid = {27508061},
title = {{From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.}},
volume = {5},
year = {2016}
}

@article{frazee2011,
	title = {{ReCount}: a multi-experiment resource of analysis-ready {RNA}-seq gene count datasets},
	volume = {12},
	issn = {1471-2105},
	shorttitle = {{ReCount}},
	doi = {10.1186/1471-2105-12-449},
	journal = {BMC bioinformatics},
	author = {Frazee, Alyssa C. and Langmead, Ben and Leek, Jeffrey T.},
	year = {2011},
	pages = {449}
}

@Article{airway,
    author = {{Himes} and B. E. and {Jiang} and {X.} and {Wagner} and {P.} and {Hu} and {R.} and {Wang} and {Q.} and {Klanderman} and {B.} and {Whitaker} and R. M. and {Duan} and {Q.} and {Lasky-Su} and {J.} and {Nikolos} and {C.} and {Jester} and {W.} and {Johnson} and {M.} and {Panettieri} and R. A. and {Tantisira} and K. G. and {Weiss} and S. T. and {Lu} and {Q.}},
    title = {{{R}{N}{A}-{S}eq {T}ranscriptome {P}rofiling {I}dentifies {C}{R}{I}{S}{P}{L}{D}2 as a {G}lucocorticoid {R}esponsive {G}ene that {M}odulates {C}ytokine {F}unction in {A}irway {S}mooth {M}uscle {C}ells}},
    journal = {PLoS ONE},
    year = {2014},
    volume = {9},
    number = {6},
    pages = {e99625}
  }
  
  
@Manual{summarizedexperiment,
    title = {SummarizedExperiment: SummarizedExperiment container},
    author = {Martin Morgan and Valerie Obenchain and Jim Hester and Herv{\'e} Pag{\`e}s},
    year = {2017},
    note = {R package version 1.6.3},
}

@article{Wilks2017,
author = {Wilks, Christopher and Gaddipati, Phani and Nellore, Abhinav and Langmead, Benjamin},
doi = {10.1101/097881},
journal = {bioRxiv},
title = {{Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples}},
year = {2017}
}


@article{rail2016,
	title = {Rail-{RNA}: scalable analysis of {RNA}-seq splicing and coverage},
	issn = {1367-4811},
	shorttitle = {Rail-{RNA}},
	doi = {10.1093/bioinformatics/btw575},
	language = {eng},
	journal = {Bioinformatics (Oxford, England)},
	author = {Nellore, Abhinav and Collado-Torres, Leonardo and Jaffe, Andrew E. and Alquicira-Hern{\'a}ndez, Jos{\'e} and Wilks, Christopher and Pritt, Jacob and Morton, James and Leek, Jeffrey T. and Langmead, Ben},
	month = sep,
	year = {2016},
	pmid = {27592709}
}

@article{lawrence2013,
  title={Software for computing and annotating genomic ranges},
  author={Lawrence, Michael and Huber, Wolfgang and Pag{\`e}s, Herv{\'e} and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert and Morgan, Martin T and Carey, Vincent J},
  journal={PLoS computational biology},
  volume={9},
  number={8},
  pages={e1003118},
  year={2013},
  publisher={Public Library of Science},
  doi = {10.1371/journal.pcbi.1003118}
}


@article{jaffe2015,
	title = {Developmental regulation of human cortex transcription and its clinical relevance at single base resolution},
	volume = {18},
	issn = {1546-1726},
	doi = {10.1038/nn.3898},
	number = {1},
	journal = {Nature Neuroscience},
	author = {Jaffe, Andrew E. and Shin, Jooheon and Collado-Torres, Leonardo and Leek, Jeffrey T. and Tao, Ran and Li, Chao and Gao, Yuan and Jia, Yankai and Maher, Brady J. and Hyde, Thomas M. and Kleinman, Joel E. and Weinberger, Daniel R.},
	month = jan,
	year = {2015},
	pages = {154--161}
}

@article {Ellis2017,
	author = {Ellis, Shannon E and Collado-Torres, Leonardo and Leek, Jeffrey},
	title = {Improving the value of public RNA-seq expression data by phenotype prediction},
	year = {2017},
	doi = {10.1101/145656},
	publisher = {Cold Spring Harbor Labs Journals},
	journal = {bioRxiv}
}

@article{law2014voom,
  title={Voom: precision weights unlock linear model analysis tools for RNA-seq read counts},
  author={Law, Charity W and Chen, Yunshun and Shi, Wei and Smyth, Gordon K},
  journal={Genome Biol},
  volume={15},
  number={2},
  pages={R29},
  year={2014}
}

@article{collado2016regionreport,
	title = {{regionReport}: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]},
	doi = {10.12688/f1000research.6379.2},
	journal = {F1000Research},
	author = {Collado-Torres, Leonardo and Jaffe, Andrew E. and Leek, Jeffrey T.},
	month = jun,
	year = {2016},
    volume = {4},
    pages = {1--10}
}

@article{love2014moderated,
  title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
  journal={Genome biology},
  volume={15},
  number={12},
  pages={1--21},
  year={2014},
  publisher={Springer}
}

@article{robinson2010,
	title = {{edgeR:} a Bioconductor package for differential expression analysis of digital gene expression data},
	volume = {26},
	issn = {1367-4811},
	shorttitle = {{edgeR}},
	doi = {10.1093/bioinformatics/btp616},
	language = {eng},
	number = {1},
	journal = {Bioinformatics (Oxford, England)},
	author = {Robinson, Mark D and {McCarthy}, Davis J and Smyth, Gordon K},
	month = jan,
	year = {2010},
	pages = {139--140}
}

@Manual{ideal,
    title = {ideal: Interactive Differential Expression AnaLysis},
    author = {Federico Marini},
    year = {2017},
    note = {R package version 1.0.0}
  }

@Article{clusterProfiler,
    title = {clusterProfiler: an R package for comparing biological themes among gene clusters},
    author = {Guangchuang Yu and Li-Gen Wang and Yanyan Han and Qing-Yu He},
    journal = {OMICS: A Journal of Integrative Biology},
    year = {2012},
    volume = {16},
    number = {5},
    pages = {284-287},
    pmid = {22455463},
    doi = {10.1089/omi.2011.0118},
  }
  

@article{Soneson2015,
    author = {Soneson, Charlotte and Love, Michael I. and Robinson, Mark D.},
    doi = {10.12688/f1000research.7563.2},
    issn = {2046-1402},
    journal = {F1000Research},
    number = {0},
    pages = {1521},
    pmid = {26925227},
    title = {{Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. [version 2; referees: 2 approved]}},
    volume = {4},
    year = {2015}
}

@Manual{epivizr,
    title = {epivizr: R Interface to epiviz web app},
    author = {Hector Corrada Bravo and Florin Chelaru and Llewellyn Smith and Naomi Goldstein and Jayaram Kancherla and Morgan Walter and Brian Gottfried},
    year = {2017},
    note = {R package version 2.6.0},
}
  
@Manual{wiggleplotr,
    title = {wiggleplotr: Make read coverage plots from BigWig files},
    author = {Kaur Alasoo},
    year = {2017},
    note = {R package version 1.0.0},
}

@Article{bumphunter,
    author = {Andrew E. Jaffe and Peter Murakami and Hwajin Lee and Jeffrey T. Leek and Daniele M. Fallin and Andrew P. Feinberg and Rafael A. Irizarry},
    title = {Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies},
    journal = {International journal of epidemiology},
    year = {2012},
    volume = {41},
    number = {1},
    pages = {200--209},
    doi = {10.1093/ije/dyr238},
    pubmed = {22422453},
}

@article{jaffe2017,
    author = {Andrew E. Jaffe and Richard Straub and Joo Heon Shin and Ran Tao and Yuan Gao and Leonardo Collado-Torres and Tony Kam-Thong and Hualin S Xi and Jie Quan and Qiang Chen and Carlo Colantuoni and Bill Ulrich and Brady J. Maher and Amy Depp-Soboslay and The BrainSeq Consortium and Alan Cross and Nicholas J. Brandon and Jeffrey T. Leek and Thomas M. Hyde and Joel E. Kleinman and Daniel R. Weinberger},
    journal = {bioRxiv},
    title = {{Developmental and genetic regulation of the human cortex transcriptome in schizophrenia}},
    year = {2017}
}

@Article{rtracklayer,
    title = {rtracklayer: an R package for interfacing with
              genome browsers},
    author = {Michael Lawrence and Robert Gentleman and Vincent Carey},
    year = {2009},
    journal = {Bioinformatics},
    volume = {25},
    pages = {1841-1842},
    doi = {10.1093/bioinformatics/btp328}
}

@article{huber2015,
  title={Orchestrating high-throughput genomic analysis with Bioconductor},
  author={Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and others},
  journal={Nature methods},
  volume={12},
  number={2},
  pages={115--121},
  year={2015},
  publisher={Nature Publishing Group},
  doi = {10.1038/nmeth.3252}
}

@Article{TCGAbiolinks,
    title = { TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data},
    author = {Antonio Colaprico and Tiago Chedraoui Silva and Catharina Olsen and Luciano Garofano and Claudia Cava and Davide Garolini and Thais Sabedot and Tathiane M. Malta and Stefano M. Pagnotta and Isabella Castiglioni and Michele Ceccarelli and Gianluca Bontempi and Houtan Noushmehr},
    journal = {Nucleic Acids Research},
    year = {2015},
    journal = {Nucleic Acids Research},
    doi = {10.1093/nar/gkv1507}
}

@article{recountWorkflow,
	title = {recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]},
	doi = {10.12688/f1000research.12223.1},
	journal = {F1000Research},
	author = {Collado-Torres, Leonardo and Nellore, Abhinav and Jaffe, Andrew E.},
	month = aug,
	year = {2017},
    volume = {6},
    NUMBER = {1558}
}