% 20179076 
@Article{pmid20179076,
   Author="Yu, G.  and Li, F.  and Qin, Y.  and Bo, X.  and Wu, Y.  and Wang, S. ",
   Title="{{G}{O}{S}em{S}im: an {R} package for measuring semantic similarity among {G}{O} terms and gene products}",
   Journal="Bioinformatics",
   Year="2010",
   Volume="26",
   Number="7",
   Pages="976--978",
   Month="Apr"
}

% 26209431 
@Article{pmid26209431,
   Author="Galili, T. ",
   Title="{dendextend: an {R} package for visualizing, adjusting and comparing trees of hierarchical clustering}",
   Journal="Bioinformatics",
   Year="2015",
   Volume="31",
   Number="22",
   Pages="3718--3720",
   Month="Nov"
}

% 21115458 
@Article{pmid21115458,
   Author="Maglott, D.  and Ostell, J.  and Pruitt, K. D.  and Tatusova, T. ",
   Title="{{E}ntrez {G}ene: gene-centered information at {N}{C}{B}{I}}",
   Journal="Nucleic Acids Res.",
   Year="2011",
   Volume="39",
   Number="Database issue",
   Pages="D52--57",
   Month="Jan"
}

% 24063302 
@Article{pmid24063302,
   Author="Fong, J. H.  and Murphy, T. D.  and Pruitt, K. D. ",
   Title="{{C}omparison of {R}ef{S}eq protein-coding regions in human and vertebrate genomes}",
   Journal="BMC Genomics",
   Year="2013",
   Volume="14",
   Pages="654",
   Month="Sep"
}

% AnnotationForge 
@Manual{AnnotationForge,
    title = {AnnotationForge: Code for Building Annotation Database Packages},
    author = {Marc Carlson and Herve Pages},
    year = {2017},
    note = {R package version 1.18.0},
 }

% E-utilities
@Manual{E-utilities,
    title = {Entrez Programming Utilities Help},
    author = {Eric Sayers},
    year = {2013},
    note = {https://www.ncbi.nlm.nih.gov/books/NBK25500/},
 }

% 25378336 
@Article{pmid25378336,
   Author="Huntley, R. P.  and Sawford, T.  and Mutowo-Meullenet, P.  and Shypitsyna, A.  and Bonilla, C.  and Martin, M. J.  and O'Donovan, C. ",
   Title="{{T}he {G}{O}{A} database: gene {O}ntology annotation updates for 2015}",
   Journal="Nucleic Acids Res.",
   Year="2015",
   Volume="43",
   Number="Database issue",
   Pages="D1057--1063",
   Month="Jan"
}

% 19617889 
@Article{pmid19617889,
   Author="Durinck, S.  and Spellman, P. T.  and Birney, E.  and Huber, W. ",
   Title="{{M}apping identifiers for the integration of genomic datasets with the {R}/{B}ioconductor package bioma{R}t}",
   Journal="Nat Protoc",
   Year="2009",
   Volume="4",
   Number="8",
   Pages="1184--1191"
}

% 16082012 
@Article{pmid16082012,
   Author="Durinck, S.  and Moreau, Y.  and Kasprzyk, A.  and Davis, S.  and De Moor, B.  and Brazma, A.  and Huber, W. ",
   Title="{{B}io{M}art and {B}ioconductor: a powerful link between biological databases and microarray data analysis}",
   Journal="Bioinformatics",
   Year="2005",
   Volume="21",
   Number="16",
   Pages="3439--3440",
   Month="Aug"
}

% DT
@Manual{DT,
    title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
    author = {Yihui Xie},
    year = {2016},
    note = {R package version 0.2},
    url = {https://CRAN.R-project.org/package=DT},
 }

% AnnotationDbi
@Manual{AnnotationDbi,
    title = {AnnotationDbi: Annotation Database Interface},
    author = {Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li},
    year = {2017},
    note = {R package version 1.38.0},
 }

% data.table
@Manual{data.table,
    title = {data.table: Extension of `data.frame`},
    author = {Matt Dowle and Arun Srinivasan},
    year = {2017},
    note = {R package version 1.10.4},
    url = {https://CRAN.R-project.org/package=data.table},
 }

% R
@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2017},
    url = {https://www.R-project.org/},
 }

% plotly
@Manual{plotly,
    title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
    author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
    year = {2017},
    note = {R package version 4.6.0},
    url = {https://CRAN.R-project.org/package=plotly},
 }

% ggplot2
@Book{ggplot2,
    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://ggplot2.org},
 }

% heatmaply
@Manual{heatmaply,
    title = {heatmaply: Interactive Cluster Heat Maps Using 'plotly'},
    author = {Tal Galili},
    year = {2017},
    note = {R package version 0.9.1},
    url = {https://CRAN.R-project.org/package=heatmaply},
 }

% dendextend
@Article{dendextend,
    author = {Tal Galili},
    title = {dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering},
    journal = {Bioinformatics},
    year = {2015},
    doi = {10.1093/bioinformatics/btv428},
    url = {http://bioinformatics.oxfordjournals.org/content/31/22/3718},
    eprint = {http://bioinformatics.oxfordjournals.org/content/31/22/3718.full.pdf+html},
  }

% dynamicTreeCut
@Manual{dynamicTreeCut,
    title = {dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms},
    author = {Peter Langfelder and Bin Zhang and with contributions from Steve Horvath},
    year = {2016},
    note = {R package version 1.63-1},
    url = {https://CRAN.R-project.org/package=dynamicTreeCut},
 }

% 18024473 
@Article{pmid18024473,
   Author="Langfelder, P.  and Zhang, B.  and Horvath, S. ",
   Title="{{D}efining clusters from a hierarchical cluster tree: the {D}ynamic {T}ree {C}ut package for {R}}",
   Journal="Bioinformatics",
   Year="2008",
   Volume="24",
   Number="5",
   Pages="719--720",
   Month="Mar"
}

% RColorBrewer
@Manual{RColorBrewer,
    title = {RColorBrewer: ColorBrewer Palettes},
    author = {Erich Neuwirth},
    year = {2014},
    note = {R package version 1.1-2},
    url = {https://CRAN.R-project.org/package=RColorBrewer},
  }

% scales
@Manual{scales,
    title = {scales: Scale Functions for Visualization},
    author = {Hadley Wickham},
    year = {2016},
    note = {R package version 0.4.1},
    url = {https://CRAN.R-project.org/package=scales},
  }

% R.utils
@Manual{R.utils,
    title = {R.utils: Various Programming Utilities},
    author = {Henrik Bengtsson},
    year = {2016},
    note = {R package version 2.5.0},
    url = {https://CRAN.R-project.org/package=R.utils},
  }

% igraph
@Article{igraph,
    title = {The igraph software package for complex network research},
    author = {Gabor Csardi and Tamas Nepusz},
    journal = {InterJournal},
    volume = {Complex Systems},
    pages = {1695},
    year = {2006},
    url = {http://igraph.org},
  }

% GO.db
@Manual{GOdb,
    title = {GO.db: A set of annotation maps describing the entire Gene Ontology},
    author = {Marc Carlson},
    year = {2017},
    note = {R package version 3.4.1},
  }

% DiagrammeR
@Manual{DiagrammeR,
    title = {DiagrammeR: Create Graph Diagrams and Flowcharts Using R},
    author = {Knut Sveidqvist and Mike Bostock and Chris Pettitt and Mike Daines and Andrei Kashcha and Richard Iannone},
    year = {2017},
    note = {R package version 0.9.0},
    url = {https://CRAN.R-project.org/package=DiagrammeR},
  }

% corrplot
@Manual{corrplot,
    title = {corrplot: Visualization of a Correlation Matrix},
    author = {Taiyun Wei and Viliam Simko},
    year = {2016},
    note = {R package version 0.77},
    url = {https://CRAN.R-project.org/package=corrplot},
  }

% devtools
@Manual{devtools,
    title = {devtools: Tools to Make Developing R Packages Easier},
    author = {Hadley Wickham and Winston Chang},
    year = {2017},
    note = {R package version 1.13.1},
    url = {https://CRAN.R-project.org/package=devtools},
  }

% 25633503 
@Article{pmid25633503,
   Author="Huber, W.  and Carey, V. J.  and Gentleman, R.  and Anders, S.  and Carlson, M.  and Carvalho, B. S.  and Bravo, H. C.  and Davis, S.  and Gatto, L.  and Girke, T.  and Gottardo, R.  and Hahne, F.  and Hansen, K. D.  and Irizarry, R. A.  and Lawrence, M.  and Love, M. I.  and MacDonald, J.  and Obenchain, V.  and Ole?, A. K.  and Pages, H.  and Reyes, A.  and Shannon, P.  and Smyth, G. K.  and Tenenbaum, D.  and Waldron, L.  and Morgan, M. ",
   Title="{{O}rchestrating high-throughput genomic analysis with {B}ioconductor}",
   Journal="Nat. Methods",
   Year="2015",
   Volume="12",
   Number="2",
   Pages="115--121",
   Month="Feb"
}

% 25378336 
@Article{pmid25378336,
   Author="Huntley, R. P.  and Sawford, T.  and Mutowo-Meullenet, P.  and Shypitsyna, A.  and Bonilla, C.  and Martin, M. J.  and O'Donovan, C. ",
   Title="{{T}he {G}{O}{A} database: gene {O}ntology annotation updates for 2015}",
   Journal="Nucleic Acids Res.",
   Year="2015",
   Volume="43",
   Number="Database issue",
   Pages="D1057--1063",
   Month="Jan"
}

% 27899575 
@Article{pmid27899575,
   Author="Aken, B. L.  and Achuthan, P.  and Akanni, W.  and Amode, M. R.  and Bernsdorff, F.  and Bhai, J.  and Billis, K.  and Carvalho-Silva, D.  and Cummins, C.  and Clapham, P.  and Gil, L.  and Giron, C. G.  and Gordon, L.  and Hourlier, T.  and Hunt, S. E.  and Janacek, S. H.  and Juettemann, T.  and Keenan, S.  and Laird, M. R.  and Lavidas, I.  and Maurel, T.  and McLaren, W.  and Moore, B.  and Murphy, D. N.  and Nag, R.  and Newman, V.  and Nuhn, M.  and Ong, C. K.  and Parker, A.  and Patricio, M.  and Riat, H. S.  and Sheppard, D.  and Sparrow, H.  and Taylor, K.  and Thormann, A.  and Vullo, A.  and Walts, B.  and Wilder, S. P.  and Zadissa, A.  and Kostadima, M.  and Martin, F. J.  and Muffato, M.  and Perry, E.  and Ruffier, M.  and Staines, D. M.  and Trevanion, S. J.  and Cunningham, F.  and Yates, A.  and Zerbino, D. R.  and Flicek, P. ",
   Title="{{E}nsembl 2017}",
   Journal="Nucleic Acids Res.",
   Year="2017",
   Volume="45",
   Number="D1",
   Pages="D635-D642",
   Month="Jan"
}

% 25355515 
@Article{pmid25355515,
   Author="Brown, G. R.  and Hem, V.  and Katz, K. S.  and Ovetsky, M.  and Wallin, C.  and Ermolaeva, O.  and Tolstoy, I.  and Tatusova, T.  and Pruitt, K. D.  and Maglott, D. R.  and Murphy, T. D. ",
   Title="{{G}ene: a gene-centered information resource at {N}{C}{B}{I}}",
   Journal="Nucleic Acids Res.",
   Year="2015",
   Volume="43",
   Number="Database issue",
   Pages="36--42",
   Month="Jan"
}

% 16606683 
@Article{pmid16606683,
   Author="Alexa, A.  and Rahnenfuhrer, J.  and Lengauer, T. ",
   Title="{{I}mproved scoring of functional groups from gene expression data by decorrelating {G}{O} graph structure}",
   Journal="Bioinformatics",
   Year="2006",
   Volume="22",
   Number="13",
   Pages="1600--1607",
   Month="Jul"
}

% 25428369 
@Article{pmid25428369,
   Author="Blake, J. A.  and Christie, K. R.  and Dolan, M. E.  and Drabkin, H. J.  and Hill, D. P.  and Ni, L.  and Sitnikov, D.  and Burgess, S.  and Buza, T.  and Gresham, C.  and McCarthy, F.  and Pillai, L.  and Wang, H.  and Carbon, S.  and Dietze, H.  and Lewis, S. E.  and Mungall, C. J.  and Munoz-Torres, M. C.  and Feuermann, M.  and Gaudet, P.  and Basu, S.  and Chisholm, R. L.  and Dodson, R. J.  and Fey, P.  and Mi, H.  and Thomas, P. D.  and Muruganujan, A.  and Poudel, S.  and Hu, J. C.  and Aleksander, S. A.  and McIntosh, B. K.  and Renfro, D. P.  and Siegele, D. A.  and Attrill, H.  and Brown, N. H.  and Tweedie, S.  and Lomax, J.  and Osumi-Sutherland, D.  and Parkinson, H.  and Roncaglia, P.  and Lovering, R. C.  and Talmud, P. J.  and Humphries, S. E.  and Denny, P.  and Campbell, N. H.  and Foulger, R. E.  and Chibucos, M. C.  and Gwinn Giglio, M.  and Chang, H. Y.  and Finn, R.  and Fraser, M.  and Mitchell, A.  and Nuka, G.  and Pesseat, S.  and Sangrador, A.  and Scheremetjew, M.  and Young, S. Y.  and Stephan, R.  and Harris, M. A.  and Oliver, S. G.  and Rutherford, K.  and Wood, V.  and Bahler, J.  and Lock, A.  and Kersey, P. J.  and McDowall, M. D.  and Staines, D. M.  and Dwinell, M.  and Shimoyama, M.  and Laulederkind, S.  and Hayman, G. T.  and Wang, S. J.  and Petri, V.  and D'Eustachio, P.  and Matthews, L.  and Balakrishnan, R.  and Binkley, G.  and Cherry, J. M.  and Costanzo, M. C.  and Demeter, J.  and Dwight, S. S.  and Engel, S. R.  and Hitz, B. C.  and Inglis, D. O.  and Lloyd, P.  and Miyasato, S. R.  and Paskov, K.  and Roe, G.  and Simison, M.  and Nash, R. S.  and Skrzypek, M. S.  and Weng, S.  and Wong, E. D.  and Berardini, T. Z.  and Li, D.  and Huala, E.  and Argasinska, J.  and Arighi, C.  and Auchincloss, A.  and Axelsen, K.  and Argoud-Puy, G.  and Bateman, A.  and Bely, B.  and Blatter, M. C.  and Bonilla, C.  and Bougueleret, L.  and Boutet, E.  and Breuza, L.  and Bridge, A.  and Britto, R.  and Casals, C.  and Cibrian-Uhalte, E.  and Coudert, E.  and Cusin, I.  and Duek-Roggli, P.  and Estreicher, A.  and Famiglietti, L.  and Gane, P.  and Garmiri, P.  and Gos, A.  and Gruaz-Gumowski, N.  and Hatton-Ellis, E.  and Hinz, U.  and Hulo, C.  and Huntley, R.  and Jungo, F.  and Keller, G.  and Laiho, K.  and Lemercier, P.  and Lieberherr, D.  and MacDougall, A.  and Magrane, M.  and Martin, M.  and Masson, P.  and Mutowo, P.  and O'Donovan, C.  and Pedruzzi, I.  and Pichler, K.  and Poggioli, D.  and Poux, S.  and Rivoire, C.  and Roechert, B.  and Sawford, T.  and Schneider, M.  and Shypitsyna, A.  and Stutz, A.  and Sundaram, S.  and Tognolli, M.  and Wu, C.  and Xenarios, I.  and Chan, J.  and Kishore, R.  and Sternberg, P. W.  and Van Auken, K.  and Muller, H. M.  and Done, J.  and Li, Y.  and Howe, D.  and Westerfield, M. ",
   Title="{{G}ene {O}ntology {C}onsortium: going forward}",
   Journal="Nucleic Acids Res.",
   Year="2015",
   Volume="43",
   Number="Database issue",
   Pages="D1049--1056",
   Month="Jan"
}

% 25730472 
@Article{pmid25730472,
   Author="Fu, N. Y.  and Rios, A. C.  and Pal, B.  and Soetanto, R.  and Lun, A. T.  and Liu, K.  and Beck, T.  and Best, S. A.  and Vaillant, F.  and Bouillet, P.  and Strasser, A.  and Preiss, T.  and Smyth, G. K.  and Lindeman, G. J.  and Visvader, J. E. ",
   Title="{{E}{G}{F}-mediated induction of {M}cl-1 at the switch to lactation is essential for alveolar cell survival}",
   Journal="Nat. Cell Biol.",
   Year="2015",
   Volume="17",
   Number="4",
   Pages="365--375",
   Month="Apr"
}

% 23104842 
@Article{pmid23104842,
   Author="Lund, S. P.  and Nettleton, D.  and McCarthy, D. J.  and Smyth, G. K. ",
   Title="{{D}etecting differential expression in {R}{N}{A}-sequence data using quasi-likelihood with shrunken dispersion estimates}",
   Journal="Stat Appl Genet Mol Biol",
   Year="2012",
   Volume="11",
   Number="5",
   Month="Oct"
}

% edgeR
@manual{edgeR,
 title = {edgeRUsersGuide},
 author = {Chen, Y. and McCarthy, D. and Ritchie, M. and Robinson, M. and Smyth, G. K.},    
 note= {http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf}
}

