bachelor-thesis.bib

@online{morpheus,
  author = {Joshua Gould},
  title = {morpheus.js},
  howpublished = "[Электронный ресурс]",
  url = "https://clue.io/morpheus.js/"
}

@online{genee,
  author = {Joshua Gould},
  title = {GENE-E},
  howpublished = "[Электронный ресурс]",
  url = "http://www.broadinstitute.org/cancer/software/GENE-E/"
}

@Article{opencpu,
    title = {The OpenCPU System: Towards a Universal Interface for
      Scientific Computing through Separation of Concerns},
    author = {Jeroen Ooms},
    journal = {arXiv:1406.4806 [stat.CO]},
    year = {2014},
    url = {http://arxiv.org/abs/1406.4806},
  }

@article{docker,
 author = {Merkel, Dirk},
 title = {Docker: Lightweight Linux Containers for Consistent Development and Deployment},
 journal = {Linux J.},
 issue_date = {March 2014},
 volume = {2014},
 number = {239},
 month = mar,
 year = {2014},
 issn = {1075-3583},
 articleno = {2},
 url = {http://dl.acm.org/citation.cfm?id=2600239.2600241},
 acmid = {2600241},
 publisher = {Belltown Media},
 address = {Houston, TX},
} 


@article{protobuf,
  title={Protocol buffers: Google’s data interchange format},
  author={Varda, Kenton},
  journal={Google Open Source Blog, Available at least as early as Jul},
  year={2008}
}

@Manual{rproject,
     title = {R: A Language and Environment for Statistical Computing},
     author = {{R Core Team}},
     organization = {R Foundation for Statistical Computing},
     address = {Vienna, Austria},
     year = {2014},
     url = {http://www.R-project.org/},
   }

@book{nodejs,
 author = {Surhone, Lambert M. and Tennoe, Mariam T. and Henssonow, Susan F.},
 title = {Node.Js},
 year = {2010},
 isbn = {6133180196, 9786133180192},
 publisher = {Betascript Publishing},
 address = {Mauritius},
} 


@online{apache,
  title = {Apache HTTP Server Project},
  howpublished = "[Электронный ресурс]",
  url = "https://httpd.apache.org"
}

@online{dhub,
  title = {Docker Hub},
  howpublished = "[Электронный ресурс]",
  url = "https://hub.docker.com/"
}

@online{github,
  title = {GitHub},
  howpublished = "[Электронный ресурс]",
  url = "https://github.com/"
}

@online{bitbucket,
  title = {Bitbucket},
  howpublished = "[Электронный ресурс]",
  url = "https://bitbucket.org/"
}

@Manual{maf,
  title = "{Mutation Annotation Format}",
  howpublished = "[Электронный ресурс]",
  url = "https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification/"
}

@Manual{gct,
  title = {GCT},
  howpublished = "[Электронный ресурс]",
  url = "http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#GCT/"
}

@Manual{gmt,
  title = {Gene Matrix Transposed file format},
  howpublished = "[Электронный ресурс]",
  url = "http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29/"
}

@Article{tcga,
author={Network, The Cancer Genome Atlas Research
and Weinstein, John N.
and Collisson, Eric A.
and Mills, Gordon B.
and Shaw, Kenna R. Mills
and Ozenberger, Brad A.
and Ellrott, Kyle
and Shmulevich, Ilya
and Sander, Chris
and Stuart, Joshua M.},
title={The Cancer Genome Atlas Pan-Cancer analysis project},
journal={Nat Genet},
year={2013},
month={Oct},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
volume={45},
number={10},
pages={1113-1120},
abstract={The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.},
note={Commentary},
issn={1061-4036},
url={http://dx.doi.org/10.1038/ng.2764}
}

@book{ajax,
 author = {Holdener, III, Anthony T.},
 title = {Ajax: The Definitive Guide},
 year = {2008},
 isbn = {9780596528386},
 edition = {First},
 publisher = {O'Reilly},
} 

@online{protobufjs,
  author = {dcode},
  title = {Protocol Buffers for JavaScript (\& TypeScript)},
  howpublished = "[Электронный ресурс]",
  url = "https://github.com/dcodeIO/ProtoBuf.js/"
}

@online{plotly, 
author = {Plotly Technologies Inc.},
title = {Collaborative data science},
publisher = {Plotly Technologies Inc.},
address = {Montréal, QC},
year = {2015},
url = {https://plot.ly}
}

@Manual{expressionset,
  author = {Seth Falcon and Martin Morgan and Robert Gentleman},
  year = {2006},
  title = {An Introduction to Bioconductor’s ExpressionSet Class},
  howpublished = "[Электронный ресурс]",
  url = "https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf"
}

@Article{biobase,
  author = {{Huber} and {W.} and {Carey} and V. J. and {Gentleman} and {R.} and {Anders} and {S.} and {Carlson} and {M.} and {Carvalho} and B. S. and {Bravo} and H. C. and {Davis} and {S.} and {Gatto} and {L.} and {Girke} and {T.} and {Gottardo} and {R.} and {Hahne} and {F.} and {Hansen} and K. D. and {Irizarry} and R. A. and {Lawrence} and {M.} and {Love} and M. I. and {MacDonald} and {J.} and {Obenchain} and {V.} and {{Ole's}} and A. K. and {{Pag`es}} and {H.} and {Reyes} and {A.} and {Shannon} and {P.} and {Smyth} and G. K. and {Tenenbaum} and {D.} and {Waldron} and {L.} and {Morgan} and {M.}},
  title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
  journal = {Nature Methods},
  year = {2015},
  volume = {12},
  number = {2},
  pages = {115--121},
  url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
}

@Article{geoquery,
  author = {Sean Davis and Paul Meltzer},
  title = {GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor},
  journal = {Bioinformatics},
  year = {2007},
  volume = {14},
  pages = {1846--1847},
}

@Article{limma,
  author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
  title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
  journal = {Nucleic Acids Research},
  year = {2015},
  volume = {43},
  number = {7},
  pages = {e47},
}

@Manual{protolite,
    title = {protolite: Fast and Simple Object Serialization to Protocol Buffers},
    author = {Jeroen Ooms},
    year = {2017},
    note = {R package version 1.6},
    url = {https://CRAN.R-project.org/package=protolite},
  }


@Manual{stats,
  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/},
}

@Manual{shiny,
    title = {shiny: Web Application Framework for R},
    author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
    year = {2017},
    note = {R package version 1.0.3},
    url = {https://CRAN.R-project.org/package=shiny},
  }

@techreport{http,
  title={Hypertext transfer protocol--HTTP/1.1},
  author={Fielding, Roy and Gettys, Jim and Mogul, Jeffrey and Frystyk, Henrik and Masinter, Larry and Leach, Paul and Berners-Lee, Tim},
  year={1999}
}

@misc{projectx,
title = {Проектирование и реализация веб-сервиса для анализа экспрессии генов},
author = {Константин Зайцев},
year = {2015},
url = {http://is.ifmo.ru/diploma-theses/2015/bachelor/zaycev/zaycev.pdf},
langid = {russian}
}

@article{geo,
  title={Gene Expression Omnibus: NCBI gene expression and hybridization array data repository},
  author={Edgar, Ron and Domrachev, Michael and Lash, Alex E},
  journal={Nucleic acids research},
  volume={30},
  number={1},
  pages={207--210},
  year={2002},
  publisher={Oxford Univ Press}
}

@Manual{rapache,
	title = {rApache: Web application development with R and Apache.},
	author = {Jeffrey Horner},
	year = {2013},
	url = {http://www.rapache.net/},
}

@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},
  }