% Wood2014-vs
@ARTICLE{kraken,
  title    = "Kraken: ultrafast metagenomic sequence classification using exact
              alignments",
  author   = "Wood, Derrick E and Salzberg, Steven L",
  journal  = "Genome Biol.",
  volume   =  15,
  number   =  3,
  pages    = "R46",
  month    =  mar,
  year     =  2014,
  url      = "http://dx.doi.org/10.1186/gb-2014-15-3-r46",
  language = "en",
  issn     = "1465-6906",
  pmid     = "24580807",
  doi      = "10.1186/gb-2014-15-3-r46",
  pmc      = "PMC4053813"
}

% Yang2002-sx
@ARTICLE{Yang:2002ty,
  title       = "Normalization for {cDNA} microarray data: a robust composite
                 method addressing single and multiple slide systematic
                 variation",
  author      = "Yang, Yee Hwa and Dudoit, Sandrine and Luu, Percy and Lin,
                 David M and Peng, Vivian and Ngai, John and Speed, Terence P",
  affiliation = "Department of Statistics, Helen Wills Neuroscience Institute,
                 University of California, Berkeley, CA 94720-3860, USA.",
  journal     = "Nucleic Acids Res.",
  volume      =  30,
  number      =  4,
  pages       = "e15",
  month       =  feb,
  year        =  2002,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/11842121",
  language    = "en",
  issn        = "0305-1048, 1362-4962",
  pmid        = "11842121",
  pmc         = "PMC100354"
}

% Love2016-ht
@ARTICLE{Love:2015kw,
  title    = "{RNA-Seq} workflow: gene-level exploratory analysis and
              differential expression",
  author   = "Love, Michael I and Anders, Simon and Kim, Vladislav and Huber,
              Wolfgang",
  journal  = "F1000Res.",
  volume   =  4,
  month    =  nov,
  year     =  2016,
  url      = "https://f1000research.com/articles/4-1070/v2/pdf",
  doi      = "10.12688/f1000research.7035.2"
}

% Dobin2013-hr
@ARTICLE{STAR,
  title       = "{STAR}: ultrafast universal {RNA-seq} aligner",
  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",
  affiliation = "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
                 dobin@cshl.edu",
  journal     = "Bioinformatics",
  volume      =  29,
  number      =  1,
  pages       = "15--21",
  month       =  jan,
  year        =  2013,
  url         = "http://dx.doi.org/10.1093/bioinformatics/bts635",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "23104886",
  doi         = "10.1093/bioinformatics/bts635",
  pmc         = "PMC3530905"
}

% Dobin2016-qj
@ARTICLE{Dobin:2016kq,
  title       = "Optimizing {RNA-Seq} Mapping with {STAR}",
  author      = "Dobin, Alexander and Gingeras, Thomas R",
  affiliation = "Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring
                 Harbor, NY, 11746, USA. dobin@cshl.edu. Cold Spring Harbor
                 Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11746,
                 USA.",
  journal     = "Methods Mol. Biol.",
  volume      =  1415,
  pages       = "245--262",
  year        =  2016,
  url         = "http://dx.doi.org/10.1007/978-1-4939-3572-7_13",
  language    = "en",
  issn        = "1064-3745, 1940-6029",
  pmid        = "27115637",
  doi         = "10.1007/978-1-4939-3572-7\_13"
}

% Kolde2015-dy
@MANUAL{pheatmap,
  title  = "pheatmap: Pretty Heatmaps",
  author = "Kolde, Raivo",
  year   =  2015,
  url    = "https://CRAN.R-project.org/package=pheatmap"
}

% Andrews2010-fq
@MANUAL{fastqc,
  title  = "{FastQC}: a quality control tool for high throughput sequence data",
  author = "Andrews, Simon",
  year   =  2010,
  url    = "http://www.bioinformatics.babraham.ac.uk/projects/fastq"
}

% Conesa2016-uj
@ARTICLE{Conesa:2016du,
  title       = "A survey of best practices for {RNA-seq} data analysis",
  author      = "Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and
                 Gomez-Cabrero, David and Cervera, Alejandra and McPherson,
                 Andrew and Szcze{\'s}niak, Micha{\l} Wojciech and Gaffney,
                 Daniel J and Elo, Laura L and Zhang, Xuegong and Mortazavi,
                 Ali",
  affiliation = "Institute for Food and Agricultural Sciences, Department of
                 Microbiology and Cell Science, University of Florida,
                 Gainesville, FL, 32603, USA. aconesa@ufl.edu. Centro de
                 Investigaci{\'o}n Pr{\'\i}ncipe Felipe, Genomics of Gene
                 Expression Laboratory, 46012, Valencia, Spain.
                 aconesa@ufl.edu. Wellcome Trust Sanger Institute, Wellcome
                 Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
                 pm12@sanger.ac.uk. Wellcome Trust-Medical Research Council
                 Cambridge Stem Cell Institute, Anne McLaren Laboratory for
                 Regenerative Medicine, Department of Surgery, University of
                 Cambridge, Cambridge, CB2 0SZ, UK. pm12@sanger.ac.uk. Centro
                 de Investigaci{\'o}n Pr{\'\i}ncipe Felipe, Genomics of Gene
                 Expression Laboratory, 46012, Valencia, Spain. Department of
                 Applied Statistics, Operations Research and Quality,
                 Universidad Polit{\'e}cnica de Valencia, 46020, Valencia,
                 Spain. Unit of Computational Medicine, Department of Medicine,
                 Karolinska Institutet, Karolinska University Hospital, 171 77,
                 Stockholm, Sweden. Center for Molecular Medicine, Karolinska
                 Institutet, 17177, Stockholm, Sweden. Unit of Clinical
                 Epidemiology, Department of Medicine, Karolinska University
                 Hospital, L8, 17176, Stockholm, Sweden. Science for Life
                 Laboratory, 17121, Solna, Sweden. Systems Biology Laboratory,
                 Institute of Biomedicine and Genome-Scale Biology Research
                 Program, University of Helsinki, 00014, Helsinki, Finland.
                 School of Computing Science, Simon Fraser University, Burnaby,
                 V5A 1S6, BC, Canada. Department of Bioinformatics, Institute
                 of Molecular Biology and Biotechnology, Adam Mickiewicz
                 University in Pozna{\'n}, 61-614, Pozna{\'n}, Poland. Wellcome
                 Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge, CB10 1SA, UK. Turku Centre for Biotechnology,
                 University of Turku and {\AA}bo Akademi University, FI-20520,
                 Turku, Finland. Key Lab of Bioinformatics/Bioinformatics
                 Division, TNLIST and Department of Automation, Tsinghua
                 University, Beijing, 100084, China. School of Life Sciences,
                 Tsinghua University, Beijing, 100084, China. Department of
                 Developmental and Cell Biology, University of California,
                 Irvine, Irvine, CA, 92697-2300, USA. ali.mortazavi@uci.edu.
                 Center for Complex Biological Systems, University of
                 California, Irvine, Irvine, CA, 92697, USA.
                 ali.mortazavi@uci.edu.",
  journal     = "Genome Biol.",
  volume      =  17,
  pages       = "13",
  month       =  jan,
  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-0881-8",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "26813401",
  doi         = "10.1186/s13059-016-0881-8",
  pmc         = "PMC4728800"
}

% Li2012-jp
@ARTICLE{Li:2012cx,
  title       = "Volcano plots in analyzing differential expressions with
                 {mRNA} microarrays",
  author      = "Li, Wentian",
  affiliation = "The Robert S. Boas Center for Genomics and Human Genetics, The
                 Feinstein Institute for Medical Research, North Shore LIJ
                 Health System, Manhasset, 350 Community Drive, NY 11030, USA.
                 wtli2012@gmail.com",
  journal     = "J. Bioinform. Comput. Biol.",
  volume      =  10,
  number      =  6,
  pages       = "1231003",
  month       =  dec,
  year        =  2012,
  url         = "http://dx.doi.org/10.1142/S0219720012310038",
  language    = "en",
  issn        = "0219-7200, 1757-6334",
  pmid        = "23075208",
  doi         = "10.1142/S0219720012310038"
}

% RStudio_Team2016-pf
@MANUAL{RStudio,
  title        = "{RStudio}: Integrated Development Environment for {R}",
  author       = "{RStudio Team}",
  year         =  2016,
  url          = "http://www.rstudio.com/",
  address      = "Boston, MA",
  organization = "RStudio, Inc."
}

% Zhang2014-af
@ARTICLE{PEAR,
  title       = "{PEAR}: a fast and accurate Illumina {Paired-End} reAd mergeR",
  author      = "Zhang, Jiajie and Kobert, Kassian and Flouri, Tom{\'a}{\v s}
                 and Stamatakis, Alexandros",
  affiliation = "The Exelixis Lab, Scientific Computing Group, Heidelberg
                 Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35,
                 D-69118 Heidelberg, Graduate School for Computing in Medicine
                 and Life Sciences, Institut f{\"u}r Neuro- und Bioinformatik,
                 University of L{\"u}beck, 23538 L{\"u}beck and Karlsruhe
                 Institute of Technology, Institute for Theoretical
                 Informatics, Postfach 6980, 76128 Karlsruhe, Germany.",
  journal     = "Bioinformatics",
  volume      =  30,
  number      =  5,
  pages       = "614--620",
  month       =  mar,
  year        =  2014,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btt593",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "24142950",
  doi         = "10.1093/bioinformatics/btt593",
  pmc         = "PMC3933873"
}

% Pimentel2017-qf
@ARTICLE{sleuth,
  title       = "Differential analysis of {RNA-seq} incorporating
                 quantification uncertainty",
  author      = "Pimentel, Harold and Bray, Nicolas L and Puente, Suzette and
                 Melsted, P{\'a}ll and Pachter, Lior",
  affiliation = "Department of Computer Science, University of California,
                 Berkeley, Berkeley, California, USA. Innovative Genomics
                 Institute and Department of Molecular \&Cell Biology,
                 University of California, Berkeley, Berkeley, California, USA.
                 Department of Statistics, University of California, Berkeley,
                 Berkeley, California, USA. Faculty of Industrial Engineering,
                 Mechanical Engineering and Computer Science, University of
                 Iceland, Reykjav{\'\i}k, Iceland. Division of Biology and
                 Biological Engineering, Caltech, Pasadena, California, USA.",
  journal     = "Nat. Methods",
  volume      =  14,
  number      =  7,
  pages       = "687--690",
  month       =  jul,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nmeth.4324",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28581496",
  doi         = "10.1038/nmeth.4324"
}

% Soneson2016-tu
@ARTICLE{tximport,
  title    = "Differential analyses for {RNA-seq}: transcript-level estimates
              improve gene-level inferences",
  author   = "Soneson, Charlotte and Love, Michael I and Robinson, Mark D",
  journal  = "F1000Res.",
  volume   =  4,
  month    =  dec,
  year     =  2016,
  url      = "https://f1000research.com/articles/4-1521/v1/pdf",
  doi      = "10.12688/f1000research.7563.1"
}

% Staedtler2013-ya
@ARTICLE{Staedtler:2013eg,
  title       = "Robust and tissue-independent gender-specific transcript
                 biomarkers",
  author      = "Staedtler, Frank and Hartmann, Nicole and Letzkus, Martin and
                 Bongiovanni, Sandrine and Scherer, Andreas and Marc, Philippe
                 and Johnson, Keith J and Schumacher, Martin M",
  affiliation = "Novartis Institutes for BioMedical Research (NIBR), Biomarker
                 Development, Basel, Switzerland. Frank.Staedtler@novartis.com",
  journal     = "Biomarkers",
  volume      =  18,
  number      =  5,
  pages       = "436--445",
  month       =  aug,
  year        =  2013,
  url         = "http://dx.doi.org/10.3109/1354750X.2013.811538",
  language    = "en",
  issn        = "1354-750X, 1366-5804",
  pmid        = "23829492",
  doi         = "10.3109/1354750X.2013.811538"
}

% Patro2014-qz
@ARTICLE{sailfish,
  title       = "Sailfish enables alignment-free isoform quantification from
                 {RNA-seq} reads using lightweight algorithms",
  author      = "Patro, Rob and Mount, Stephen M and Kingsford, Carl",
  affiliation = "Lane Center for Computational Biology, School of Computer
                 Science, Carnegie Mellon University, Pittsburgh, Pennsylvania,
                 USA. 1] Department of Cell Biology and Molecular Genetics,
                 University of Maryland, College Park, Maryland, USA. [2]
                 Center for Bioinformatics and Computational Biology,
                 University of Maryland, College Park, Maryland, USA.",
  journal     = "Nat. Biotechnol.",
  volume      =  32,
  number      =  5,
  pages       = "462--464",
  month       =  may,
  year        =  2014,
  url         = "http://dx.doi.org/10.1038/nbt.2862",
  language    = "en",
  issn        = "1087-0156, 1546-1696",
  pmid        = "24752080",
  doi         = "10.1038/nbt.2862",
  pmc         = "PMC4077321"
}

% Patro2017-pi
@ARTICLE{salmon,
  title       = "Salmon provides fast and bias-aware quantification of
                 transcript expression",
  author      = "Patro, Rob and Duggal, Geet and Love, Michael I and Irizarry,
                 Rafael A and Kingsford, Carl",
  affiliation = "Department of Computer Science, Stony Brook University, Stony
                 Brook, New York, USA. DNAnexus, Mountain View, California,
                 USA. Department of Biostatistics and Computational Biology,
                 Dana-Farber Cancer Institute, Cambridge, Massachusetts, USA.
                 Department of Biostatistics, Harvard T.H. Chan School of
                 Public Health, Cambridge, Massachusetts, USA. Computational
                 Biology Department, Carnegie Mellon University, Pittsburgh,
                 Pennsylvania, USA.",
  journal     = "Nat. Methods",
  volume      =  14,
  number      =  4,
  pages       = "417--419",
  month       =  apr,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nmeth.4197",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28263959",
  doi         = "10.1038/nmeth.4197"
}

% Liao2014-js
@ARTICLE{featureCounts,
  title       = "featureCounts: an efficient general purpose program for
                 assigning sequence reads to genomic features",
  author      = "Liao, Yang and Smyth, Gordon K and Shi, Wei",
  affiliation = "Bioinformatics Division, The Walter and Eliza Hall Institute
                 of Medical Research, 1G Royal Parade, Parkville, VIC 3052,
                 Department of Computing and Information Systems and Department
                 of Mathematics and Statistics, The University of Melbourne,
                 Parkville, VIC 3010, Australia.",
  journal     = "Bioinformatics",
  volume      =  30,
  number      =  7,
  pages       = "923--930",
  month       =  apr,
  year        =  2014,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btt656",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "24227677",
  doi         = "10.1093/bioinformatics/btt656"
}

% Van_den_Berge2017-xy
@UNPUBLISHED{VandenBerge:2017fe,
  title    = "A general and powerful stage-wise testing procedure for
              differential expression and differential transcript usage",
  author   = "Van den Berge, Koen and Soneson, Charlotte and Robinson, Mark D
              and Clement, Lieven",
  journal  = "bioRxiv",
  pages    = "109082",
  month    =  feb,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/02/16/109082",
  language = "en",
  doi      = "10.1101/109082"
}

% Cui2003-rn
@ARTICLE{Cui:2003kh,
  title       = "Statistical tests for differential expression in {cDNA}
                 microarray experiments",
  author      = "Cui, Xiangqin and Churchill, Gary A",
  affiliation = "The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine
                 04609, USA.",
  journal     = "Genome Biol.",
  volume      =  4,
  number      =  4,
  pages       = "210",
  month       =  mar,
  year        =  2003,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/12702200",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "12702200",
  pmc         = "PMC154570"
}

% Langaas:2005vn
@ARTICLE{Langaas2005-zl,
  title     = "Estimating the Proportion of True Null Hypotheses, with
               Application to {DNA} Microarray Data",
  author    = "Langaas, Mette and Lindqvist, Bo Henry and Ferkingstad, Egil",
  journal   = "J. R. Stat. Soc. Series B Stat. Methodol.",
  publisher = "[Royal Statistical Society, Wiley]",
  volume    =  67,
  number    =  4,
  pages     = "555--572",
  year      =  2005,
  url       = "http://www.jstor.org/stable/3647644",
  issn      = "1369-7412, 1467-9868"
}

% Love2014-sq
@ARTICLE{DESeq2,
  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 Biol.",
  volume   =  15,
  number   =  12,
  pages    = "550",
  year     =  2014,
  url      = "http://dx.doi.org/10.1186/s13059-014-0550-8",
  language = "en",
  issn     = "1465-6906",
  pmid     = "25516281",
  doi      = "10.1186/s13059-014-0550-8",
  pmc      = "PMC4302049"
}

% Benjamini1995-de
@ARTICLE{Benjamini:1995ws,
  title     = "Controlling the False Discovery Rate: A Practical and Powerful
               Approach to Multiple Testing",
  author    = "Benjamini, Yoav and Hochberg, Yosef",
  journal   = "J. R. Stat. Soc. Series B Stat. Methodol.",
  publisher = "[Royal Statistical Society, Wiley]",
  volume    =  57,
  number    =  1,
  pages     = "289--300",
  year      =  1995,
  url       = "http://www.jstor.org/stable/2346101",
  issn      = "1369-7412, 0035-9246"
}

% Kolde2015-vr
@ARTICLE{GOsummaries,
  title    = "{GOsummaries}: an {R} Package for Visual Functional Annotation of
              Experimental Data",
  author   = "Kolde, Raivo and Vilo, Jaak",
  journal  = "F1000Res.",
  volume   =  4,
  month    =  aug,
  year     =  2015,
  url      = "https://f1000research.com/articles/4-574/v1/pdf",
  doi      = "10.12688/f1000research.6925.1"
}

% Ward1963-xf
@ARTICLE{WardJr:1963eu,
  title     = "Hierarchical grouping to optimize an objective function",
  author    = "Ward, Jr, Joe H",
  journal   = "Journal of the American Statistical Association",
  publisher = "Taylor \& Francis",
  volume    =  58,
  number    =  301,
  pages     = "236--244",
  year      =  1963,
  url       = "http://www.tandfonline.com/doi/abs/10.1080/01621459.1963.10500845",
  doi       = "10.1080/01621459.1963.10500845"
}

% Pantano2017-qp
@MANUAL{DEGreport,
  title  = "{DEGreport}: Report of {DEG} analysis",
  author = "Pantano, Lorena",
  year   =  2017,
  url    = "https://bioconductor.org/packages/release/bioc/html/DEGreport.html",
  doi    = "10.18129/B9.bioc.DEGreport"
}

% Hilbe2011-wh
@BOOK{Hilbe:2011ua,
  title     = "{Negative Binomial Regression}",
  author    = "Hilbe, Joseph M",
  publisher = "Cambridge University Press",
  month     =  mar,
  year      =  2011,
  url       = "https://market.android.com/details?id=book-0Q_ijxOEBjMC",
  language  = "en",
  isbn      = "9780521198158"
}

% Karyagyna2010-cx
@ARTICLE{Karyagyna:2010th,
  title       = "{Probe-Level} Universal Search ({PLUS}) algorithm for gender
                 differentiation in affymetrix datasets",
  author      = "Karyagyna, Anna S and Vassiliev, Michail O and Ershova, Anna S
                 and Nurtdinov, Ramil N and Lossev, Ilya S",
  affiliation = "NF Gamaleya Research Institute of Epidemiology and
                 Microbiology, Russian Academy of Medical Sciences, Institute
                 of Agricultural Biotechnology, Moscow, Russia.
                 akaryagina@gmail.com",
  journal     = "J. Bioinform. Comput. Biol.",
  volume      =  8,
  number      =  3,
  pages       = "553--577",
  month       =  jun,
  year        =  2010,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/20556862",
  language    = "en",
  issn        = "0219-7200, 1757-6334",
  pmid        = "20556862",
  doi         = "10.1142/S0219720010004823"
}

% Wickham2009-si
@BOOK{ggplot2,
  title     = "ggplot2: Elegant Graphics for Data Analysis",
  author    = "Wickham, Hadley",
  publisher = "Springer New York",
  series    = "Use R",
  year      =  2009,
  url       = "https://link.springer.com/book/10.1007%2F978-0-387-98141-3",
  isbn      = "9780387981406, 9780387981413",
  doi       = "10.1007/978-0-387-98141-3"
}

% Robinson2010-np
@ARTICLE{Robinson:2010dd,
  title       = "A scaling normalization method for differential expression
                 analysis of {RNA-seq} data",
  author      = "Robinson, Mark D and Oshlack, Alicia",
  affiliation = "Bioinformatics Division, Walter and Eliza Hall Institute, 1G
                 Royal Parade, Parkville, Australia. mrobinson@wehi.edu.au",
  journal     = "Genome Biol.",
  volume      =  11,
  number      =  3,
  pages       = "R25",
  month       =  mar,
  year        =  2010,
  url         = "http://dx.doi.org/10.1186/gb-2010-11-3-r25",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "20196867",
  doi         = "10.1186/gb-2010-11-3-r25",
  pmc         = "PMC2864565"
}

% Jolliffe2002-jz
@BOOK{Jolliffe:2002wx,
  title     = "{Principal component analysis}",
  author    = "Jolliffe, Ian",
  publisher = "Wiley Online Library",
  year      =  2002
}

% Wickham2007-lr
@ARTICLE{reshape2,
  title   = "Reshaping data with the reshape package",
  author  = "Wickham, Hadley",
  journal = "J. Stat. Softw.",
  volume  =  21,
  number  =  12,
  pages   = "1--20",
  year    =  2007
}

% Cox1987-dw
@ARTICLE{Cox:1987fu,
  title     = "Parameter Orthogonality and Approximate Conditional Inference",
  author    = "Cox, D R and Reid, N",
  journal   = "J. R. Stat. Soc. Series B Stat. Methodol.",
  publisher = "[Royal Statistical Society, Wiley]",
  volume    =  49,
  number    =  1,
  pages     = "1--39",
  year      =  1987,
  url       = "http://www.jstor.org/stable/2345476",
  issn      = "1369-7412, 0035-9246"
}

% Li2014-ll
@ARTICLE{Li:2014fv,
  title       = "Using volcano plots and regularized-chi statistics in genetic
                 association studies",
  author      = "Li, Wentian and Freudenberg, Jan and Suh, Young Ju and Yang,
                 Yaning",
  affiliation = "The Robert S. Boas Center for Genomics and Human Genetics, The
                 Feinstein Institute for Medical Research, North Shore LIJ
                 Health System, 350 Community Drive, Manhasset, NY 11030, USA.
                 Electronic address: wtli2012@gmail.com. The Robert S. Boas
                 Center for Genomics and Human Genetics, The Feinstein
                 Institute for Medical Research, North Shore LIJ Health System,
                 350 Community Drive, Manhasset, NY 11030, USA. Department of
                 Biostatistics, School of Medicine, Inha University, Incheon,
                 South Korea. Department of Statistics and Finance, University
                 of Science and Technology of China, Anhui, 230026 Hefei,
                 China.",
  journal     = "Comput. Biol. Chem.",
  volume      =  48,
  pages       = "77--83",
  month       =  feb,
  year        =  2014,
  url         = "http://dx.doi.org/10.1016/j.compbiolchem.2013.02.003",
  language    = "en",
  issn        = "1476-9271, 1476-928X",
  pmid        = "23602812",
  doi         = "10.1016/j.compbiolchem.2013.02.003"
}

% Wang2009-dt
@ARTICLE{Wang:2009di,
  title       = "{RNA-Seq}: a revolutionary tool for transcriptomics",
  author      = "Wang, Zhong and Gerstein, Mark and Snyder, Michael",
  affiliation = "Department of Molecular, Cellular and Developmental Biology,
                 Yale University, 219 Prospect Street, New Haven, Connecticut
                 06520, USA.",
  journal     = "Nat. Rev. Genet.",
  volume      =  10,
  number      =  1,
  pages       = "57--63",
  month       =  jan,
  year        =  2009,
  url         = "http://dx.doi.org/10.1038/nrg2484",
  language    = "en",
  issn        = "1471-0056, 1471-0064",
  pmid        = "19015660",
  doi         = "10.1038/nrg2484",
  pmc         = "PMC2949280"
}

% Okonechnikov2016-us
@ARTICLE{qualimap,
  title       = "Qualimap 2: advanced multi-sample quality control for
                 high-throughput sequencing data",
  author      = "Okonechnikov, Konstantin and Conesa, Ana and
                 Garc{\'\i}a-Alcalde, Fernando",
  affiliation = "Department of Molecular Biology, Max Planck Institute for
                 Infection Biology, D-10117, Berlin, Germany. Genomics of Gene
                 Expression Lab, Centro de Investigaci{\'o}n Pr{\'\i}ncipe
                 Felipe, 46012, Valencia, Spain and Microbiology and Cell
                 Science Department, Institute for Food and Agricultural
                 Research, University of Florida at Gainesville, FL 32611-0700,
                 USA.",
  journal     = "Bioinformatics",
  volume      =  32,
  number      =  2,
  pages       = "292--294",
  month       =  jan,
  year        =  2016,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btv566",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "26428292",
  doi         = "10.1093/bioinformatics/btv566",
  pmc         = "PMC4708105"
}

% Martin2011-nx
@ARTICLE{cutadapt,
  title    = "Cutadapt removes adapter sequences from high-throughput
              sequencing reads",
  author   = "Martin, Marcel",
  journal  = "EMBnet.journal",
  volume   =  17,
  number   =  1,
  pages    = "10--12",
  month    =  may,
  year     =  2011,
  url      = "http://journal.embnet.org/index.php/embnetjournal/article/view/200",
  language = "en",
  issn     = "2226-6089, 2226-6089",
  pmid     = "1000006697",
  doi      = "10.14806/ej.17.1.200"
}

% Craciun2016-ha
@ARTICLE{Craciun2016,
  title       = "{RNA} Sequencing Identifies Novel Translational Biomarkers of
                 Kidney Fibrosis",
  author      = "Craciun, Florin L and Bijol, Vanesa and Ajay, Amrendra K and
                 Rao, Poornima and Kumar, Ramya K and Hutchinson, John and
                 Hofmann, Oliver and Joshi, Nikita and Luyendyk, James P and
                 Kusebauch, Ulrike and Moss, Christopher L and Srivastava,
                 Anand and Himmelfarb, Jonathan and Waikar, Sushrut S and
                 Moritz, Robert L and Vaidya, Vishal S",
  affiliation = "Renal Division, Department of Medicine and. Department of
                 Pathology, Brigham and Women's Hospital, Boston,
                 Massachusetts; Department of Biostatistics and. Department of
                 Pathology and Diagnostic Investigation, Michigan State
                 University, East Lansing, Michigan; Institute for Systems
                 Biology, Seattle, Washington; Kidney Research Institute,
                 University of Washington, Seattle, Washington; and. Renal
                 Division, Department of Medicine and Department of
                 Environmental Health, Harvard T.H. Chan School of Public
                 Health, Boston, Massachusetts; Harvard Program in Therapeutic
                 Sciences, Harvard Medical School, Boston, Massachusetts
                 vvaidya@bwh.harvard.edu.",
  journal     = "J. Am. Soc. Nephrol.",
  volume      =  27,
  number      =  6,
  pages       = "1702--1713",
  month       =  jun,
  year        =  2016,
  url         = "http://dx.doi.org/10.1681/ASN.2015020225",
  language    = "en",
  issn        = "1046-6673, 1533-3450",
  pmid        = "26449608",
  doi         = "10.1681/ASN.2015020225",
  pmc         = "PMC4884105"
}

% Yu2012-ae
@ARTICLE{Yu2012,
  title       = "clusterProfiler: an {R} package for comparing biological
                 themes among gene clusters",
  author      = "Yu, Guangchuang and Wang, Li-Gen and Han, Yanyan and He,
                 Qing-Yu",
  affiliation = "Institute of Life and Health Engineering, Key Laboratory of
                 Functional Protein Research of Guangdong Higher Education
                 Institutes, Jinan University, Guangzhou, People's Republic of
                 China.",
  journal     = "OMICS",
  volume      =  16,
  number      =  5,
  pages       = "284--287",
  month       =  may,
  year        =  2012,
  url         = "http://dx.doi.org/10.1089/omi.2011.0118",
  language    = "en",
  issn        = "1536-2310, 1557-8100",
  pmid        = "22455463",
  doi         = "10.1089/omi.2011.0118",
  pmc         = "PMC3339379"
}

% Daily2017-fj
@ARTICLE{Daily2017,
  title       = "Molecular, phenotypic, and sample-associated data to describe
                 pluripotent stem cell lines and derivatives",
  author      = "Daily, Kenneth and Ho Sui, Shannan J and Schriml, Lynn M and
                 Dexheimer, Phillip J and Salomonis, Nathan and Schroll, Robin
                 and Bush, Stacy and Keddache, Mehdi and Mayhew, Christopher
                 and Lotia, Samad and Perumal, Thanneer M and Dang, Kristen and
                 Pantano, Lorena and Pico, Alexander R and Grassman, Elke and
                 Nordling, Diana and Hide, Winston and Hatzopoulos, Antonis K
                 and Malik, Punam and Cancelas, Jose A and Lutzko, Carolyn and
                 Aronow, Bruce J and Omberg, Larsson",
  affiliation = "Sage Bionetworks, Seattle, Washington 98109, USA. Department
                 of Biostatistics, Harvard T.H. Chan School of Public Health,
                 Boston, Massachusetts 02115, USA. Institute for Genome
                 Sciences and Department of Epidemiology and Public Health,
                 University of Maryland School of Medicine, Baltimore, Maryland
                 21201, USA. Department of Biomedical Informatics, Cincinnati
                 Children's Hospital, Cincinnati, Ohio 45229, USA. Division of
                 Experimental Hematology and Cancer Biology, Cincinnati
                 Children's Hospital, Cincinnati, Ohio 45229, USA. Division of
                 Human Genetics, Cincinnati Children's Hospital, Cincinnati,
                 Ohio 45229, USA. Division of Developmental Biology, Cincinnati
                 Children's Hospital, Cincinnati, Ohio 45229, USA. Gladstone
                 Institutes, San Francisco, California 94158, USA.
                 Translational Trials Development and Support Laboratory Field
                 Service, Cincinnati Children's Hospital, Cincinnati, Ohio
                 45229, USA. Cell Manipulation Laboratory, Cincinnati
                 Children's Hospital, Cincinnati, Ohio 45229, USA. Sheffield
                 Institute for Translational Neuroscience, University of
                 Sheffield, Sheffield S10 2HQ, UK. Harvard Stem Cell Institute,
                 Cambridge, Massachusetts 02138, USA. Departments of Medicine
                 and Cell and Developmental Biology, Division of Cardiovascular
                 Medicine, Vanderbilt University, Nashville, Tennessee 37232,
                 USA.",
  journal     = "Sci Data",
  volume      =  4,
  pages       = "170030",
  month       =  mar,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/sdata.2017.30",
  language    = "en",
  issn        = "2052-4463",
  pmid        = "28350385",
  doi         = "10.1038/sdata.2017.30",
  pmc         = "PMC5369318"
}

% Andrews2010-fq
@MANUAL{Andrews2010,
  title  = "{FastQC}: a quality control tool for high throughput sequence data",
  author = "Andrews, Simon",
  year   =  2010,
  url    = "http://www.bioinformatics.babraham.ac.uk/projects/fastq"
}

% Dudoit2002-sy
@ARTICLE{Dudoit2002,
  title     = "Statistical methods for identifying differentially expressed
               genes in replicated {cDNA} microarray experiments",
  author    = "Dudoit, Sandrine and Yang, Yee Hwa and Callow, Matthew J and
               Speed, Terence P",
  journal   = "Stat. Sin.",
  publisher = "Institute of Statistical Science, Academia Sinica",
  volume    =  12,
  number    =  1,
  pages     = "111--139",
  year      =  2002,
  url       = "http://www.jstor.org/stable/24307038",
  issn      = "1017-0405, 1996-8507"
}

% Huber2002-sf
@ARTICLE{Huber2002,
  title       = "Variance stabilization applied to microarray data calibration
                 and to the quantification of differential expression",
  author      = "Huber, Wolfgang and von Heydebreck, Anja and S{\"u}ltmann,
                 Holger and Poustka, Annemarie and Vingron, Martin",
  affiliation = "Department of Molecular Genome Analysis, German Cancer
                 Research Center, INF 280, Heidelberg, 69120, Germany.
                 w.huber@dkfz.de",
  journal     = "Bioinformatics",
  volume      = "18 Suppl 1",
  pages       = "S96--104",
  year        =  2002,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/12169536",
  language    = "en",
  issn        = "1367-4803",
  pmid        = "12169536"
}

% Li2015-iq
@ARTICLE{Li_norm_2015,
  title       = "Comparing the normalization methods for the differential
                 analysis of Illumina high-throughput {RNA-Seq} data",
  author      = "Li, Peipei and Piao, Yongjun and Shon, Ho Sun and Ryu, Keun Ho",
  affiliation = "College of Electrical and Computer Engineering, Chungbuk
                 National University, Cheongju-si, South Korea.
                 lipeipei0611@gmail.com. College of Electrical and Computer
                 Engineering, Chungbuk National University, Cheongju-si, South
                 Korea. pyz@dblab.chungbuk.ac.kr. College of Electrical and
                 Computer Engineering, Chungbuk National University,
                 Cheongju-si, South Korea. shon0621@gmail.com. College of
                 Electrical and Computer Engineering, Chungbuk National
                 University, Cheongju-si, South Korea.
                 khryu@dblab.chungbuk.ac.kr.",
  journal     = "BMC Bioinformatics",
  volume      =  16,
  pages       = "347",
  month       =  oct,
  year        =  2015,
  url         = "http://dx.doi.org/10.1186/s12859-015-0778-7",
  language    = "en",
  issn        = "1471-2105",
  pmid        = "26511205",
  doi         = "10.1186/s12859-015-0778-7",
  pmc         = "PMC4625728"
}

@ARTICLE{Robert2015-mj,
  title       = "Errors in {RNA-Seq} quantification affect genes of relevance
                 to human disease",
  author      = "Robert, Christelle and Watson, Mick",
  affiliation = "The Roslin Institute and Royal (Dick) School of Veterinary
                 studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
                 christelle.robert@roslin.ed.ac.uk. Edinburgh Genomics, The
                 Roslin Institute, University of Edinburgh, Easter Bush, EH25
                 9RG, UK. mick.watson@roslin.ed.ac.uk.",
  journal     = "Genome Biol.",
  volume      =  16,
  pages       = "177",
  month       =  sep,
  year        =  2015,
  url         = "http://dx.doi.org/10.1186/s13059-015-0734-x",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "26335491",
  doi         = "10.1186/s13059-015-0734-x",
  pmc         = "PMC4558956"
}

% Morgan2017-dw
@MANUAL{SummarizedExperiment,
  title  = "{SummarizedExperiment}: {SummarizedExperiment} container",
  author = "Morgan, Martin and Obenchain, Valerie and Hester, Jim and
            Pag{\`e}s, Herv{\'e}",
  year   =  2017,
  url    = "http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html",
  doi    = "10.18129/B9.bioc.SummarizedExperiment"
}

% Allaire2017-mf
@MANUAL{rmarkdown,
  title  = "rmarkdown: Dynamic Documents for {R}",
  author = "Allaire, J J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan
            and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins,
            Aron and Hyndman, Rob and Arslan, Ruben",
  year   =  2017,
  url    = "https://CRAN.R-project.org/package=rmarkdown"
}

% Ewels2016-vh
@ARTICLE{MultiQC,
  title       = "{MultiQC}: summarize analysis results for multiple tools and
                 samples in a single report",
  author      = "Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and
                 K{\"a}ller, Max",
  affiliation = "Department of Biochemistry and Biophysics, Science for Life
                 Laboratory, Stockholm University, Stockholm 106 91, Sweden.
                 Department of Molecular Medicine and Surgery, Science for Life
                 Laboratory, Center for Molecular Medicine, Karolinska
                 Institutet, Stockholm, Sweden. Science for Life Laboratory,
                 School of Biotechnology, Division of Gene Technology, Royal
                 Institute of Technology, Stockholm, Sweden.",
  journal     = "Bioinformatics",
  volume      =  32,
  number      =  19,
  pages       = "3047--3048",
  month       =  oct,
  year        =  2016,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btw354",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "27312411",
  doi         = "10.1093/bioinformatics/btw354",
  pmc         = "PMC5039924"
}

% Huber2015-nw
@ARTICLE{Bioconductor,
  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 Gottardo, Raphael and Hahne, Florian and
                 Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael
                 and Love, Michael I and MacDonald, James and Obenchain,
                 Valerie and Ole{\'s}, Andrzej K and Pag{\`e}s, Herv{\'e} and
                 Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K and
                 Tenenbaum, Dan and Waldron, Levi and Morgan, Martin",
  affiliation = "European Molecular Biology Laboratory, Heidelberg, Germany. 1]
                 Channing Division of Network Medicine, Brigham and Women's
                 Hospital and Harvard Medical School, Boston, Massachusetts,
                 USA. [2] Harvard School of Public Health, Boston,
                 Massachusetts, USA. Genentech, South San Francisco,
                 California, USA. Computational Biology Program, Fred
                 Hutchinson Cancer Research Center, Seattle, Washington, USA.
                 Department of Medical Genetics, School of Medical Sciences,
                 State University of Campinas, Campinas, Brazil. Center for
                 Bioinformatics and Computational Biology, University of
                 Maryland, College Park, Maryland, USA. Center for Cancer
                 Research, National Cancer Institute, National Institutes of
                 Health, Bethesda, Maryland, USA. Department of Biochemistry,
                 University of Cambridge, Cambridge, UK. Institute for
                 Integrative Genome Biology, University of California,
                 Riverside, Riverside, California, USA. Vaccine and Infectious
                 Disease Division, Fred Hutchinson Cancer Research Center,
                 Seattle, Washington, USA. Novartis Institutes for Biomedical
                 Research, Basel, Switzerland. 1] McKusick-Nathans Institute of
                 Genetic Medicine, Johns Hopkins University, Baltimore,
                 Maryland, USA. [2] Department of Biostatistics, Johns Hopkins
                 University, Baltimore, Maryland, USA. 1] Harvard School of
                 Public Health, Boston, Massachusetts, USA. [2] Dana-Farber
                 Cancer Institute, Boston, Massachusetts, USA. Department of
                 Environmental and Occupational Health Sciences, University of
                 Washington, Seattle, Washington, USA. 1] Walter and Eliza Hall
                 Institute of Medical Research, Parkville, Victoria, Australia.
                 [2] Department of Mathematics and Statistics, University of
                 Melbourne, Parkville, Victoria, Australia. School of Urban
                 Public Health at Hunter College, City University of New York,
                 New York, New York, USA.",
  journal     = "Nat. Methods",
  volume      =  12,
  number      =  2,
  pages       = "115--121",
  month       =  feb,
  year        =  2015,
  url         = "http://dx.doi.org/10.1038/nmeth.3252",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "25633503",
  doi         = "10.1038/nmeth.3252",
  pmc         = "PMC4509590"
}

@ARTICLE{Ewing1998-wj,
  title       = "Base-calling of automated sequencer traces using phred. I.
                 Accuracy assessment",
  author      = "Ewing, B and Hillier, L and Wendl, M C and Green, P",
  affiliation = "Department of Molecular Biotechnology, University of
                 Washington, Seattle, Washington 98195-7730, USA.",
  journal     = "Genome Res.",
  volume      =  8,
  number      =  3,
  pages       = "175--185",
  month       =  mar,
  year        =  1998,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/9521921",
  language    = "en",
  issn        = "1088-9051",
  pmid        = "9521921"
}

@ARTICLE{Ewing1998-yc,
  title       = "Base-calling of automated sequencer traces using phred. {II}.
                 Error probabilities",
  author      = "Ewing, B and Green, P",
  affiliation = "Department of Molecular Biotechnology, University of
                 Washington, Seattle, Washington 98195-7730, USA.",
  journal     = "Genome Res.",
  volume      =  8,
  number      =  3,
  pages       = "186--194",
  month       =  mar,
  year        =  1998,
  url         = "https://www.ncbi.nlm.nih.gov/pubmed/9521922",
  language    = "en",
  issn        = "1088-9051",
  pmid        = "9521922"
}
