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references.bib
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% Encoding: UTF-8
@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},
doi = {10.1093/nar/gkv007},
}
@Manual{affyio,
title = {affyio: Tools for parsing Affymetrix data files},
author = {Ben Bolstad},
year = {2019},
note = {R package version 1.54.0},
url = {https://github.com/bmbolstad/affyio},
}
@Manual{zeallot,
title = {zeallot: Multiple, Unpacking, and Destructuring Assignment},
author = {Nathan Teetor},
year = {2018},
note = {R package version 0.1.0},
url = {https://CRAN.R-project.org/package=zeallot},
}
@Manual{sys,
title = {sys: Powerful and Reliable Tools for Running System Commands in R},
author = {Jeroen Ooms},
year = {2019},
note = {R package version 3.3},
url = {https://CRAN.R-project.org/package=sys},
}
@Manual{preprocessCore,
title = {preprocessCore: A collection of pre-processing functions},
author = {Ben Bolstad},
year = {2019},
note = {R package version 1.46.0},
url = {https://github.com/bmbolstad/preprocessCore},
}
@Article{vsn,
title = {Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression},
author = {Wolfgang Huber and Anja {von Heydebreck} and Holger Sueltmann and Annemarie Poustka and Martin Vingron},
journal = {Bioinformatics},
year = {2002},
volume = {18 Suppl. 1},
pages = {S96-S104},
}
@Article{affy,
author = {Laurent Gautier and Leslie Cope and Benjamin M. Bolstad and Rafael A. Irizarry},
title = {affy---analysis of Affymetrix GeneChip data at the probe level},
journal = {Bioinformatics},
volume = {20},
number = {3},
year = {2004},
issn = {1367-4803},
pages = {307--315},
doi = {10.1093/bioinformatics/btg405},
publisher = {Oxford University Press},
address = {Oxford, UK},
}
@Manual{impute,
title = {impute: impute: Imputation for microarray data},
author = {Trevor Hastie and Robert Tibshirani and Balasubramanian Narasimhan and Gilbert Chu},
year = {2019},
note = {R package version 1.58.0},
}
@Article{pcaMethods,
title = {pcaMethods -- a Bioconductor package providing PCA methods for incomplete data},
author = {Wolfram Stacklies and Henning Redestig and Matthias Scholz and Dirk Walther and Joachim Selbig},
journal = {Bioinformatics},
year = {2007},
pages = {1164--1167},
volume = {23},
}
@Manual{mzID,
title = {mzID: An mzIdentML parser for R},
author = {Thomas Pedersen},
year = {2019},
note = {R package version 1.22.0},
}
@Manual{ncdf4,
title = {ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files},
author = {David Pierce},
year = {2019},
note = {R package version 1.17},
url = {https://CRAN.R-project.org/package=ncdf4},
}
@Manual{Rhdf5lib,
title = {Rhdf5lib: hdf5 library as an R package},
author = {Mike Smith},
year = {2019},
note = {R package version 1.6.3},
}
@Manual{waveslim,
title = {waveslim: Basic Wavelet Routines for One-, Two- And Three-Dimensional
Signal Processing},
author = {Brandon Whitcher},
year = {2019},
note = {R package version 1.7.5.1},
url = {https://CRAN.R-project.org/package=waveslim},
}
@Manual{DEoptimR,
title = {DEoptimR: Differential Evolution Optimization in Pure R},
author = {Eduardo L. T. Conceicao},
year = {2016},
note = {R package version 1.0-8},
url = {https://CRAN.R-project.org/package=DEoptimR},
}
@Article{checkmate,
title = {{checkmate}: Fast Argument Checks for Defensive R Programming},
author = {Michel Lang},
journal = {The R Journal},
year = {2017},
url = {https://journal.r-project.org/archive/2017/RJ-2017-028/index.html},
pages = {437--445},
volume = {9},
number = {1},
}
@Manual{utf8,
title = {utf8: Unicode Text Processing},
author = {Patrick O. Perry},
year = {2018},
note = {R package version 1.1.4},
url = {https://CRAN.R-project.org/package=utf8},
}
@Manual{vctrs,
title = {vctrs: Vector Helpers},
author = {Hadley Wickham and Lionel Henry and Davis Vaughan},
year = {2019},
note = {R package version 0.2.0},
url = {https://CRAN.R-project.org/package=vctrs},
}
@Manual{formatR,
title = {formatR: Format R Code Automatically},
author = {Yihui Xie},
year = {2019},
note = {R package version 1.7},
url = {https://CRAN.R-project.org/package=formatR},
}
@Manual{ini,
title = {ini: Read and Write '.ini' Files},
author = {David Valentim Dias},
year = {2018},
note = {R package version 0.3.1},
url = {https://CRAN.R-project.org/package=ini},
}
@Manual{backports,
title = {backports: Reimplementations of Functions Introduced Since R-3.0.0},
author = {Michel Lang and {R Core Team}},
year = {2019},
note = {R package version 1.1.5},
url = {https://CRAN.R-project.org/package=backports},
}
@Manual{askpass,
title = {askpass: Safe Password Entry for R, Git, and SSH},
author = {Jeroen Ooms},
year = {2019},
note = {R package version 1.1},
url = {https://CRAN.R-project.org/package=askpass},
}
@Manual{e1071,
title = {e1071: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien},
author = {David Meyer and Evgenia Dimitriadou and Kurt Hornik and Andreas Weingessel and Friedrich Leisch},
year = {2019},
note = {R package version 1.7-2},
url = {https://CRAN.R-project.org/package=e1071},
}
@Manual{gtools,
title = {gtools: Various R Programming Tools},
author = {Gregory R. Warnes and Ben Bolker and Thomas Lumley},
year = {2018},
note = {R package version 3.8.1},
url = {https://CRAN.R-project.org/package=gtools},
}
@Manual{bit,
title = {bit: A Class for Vectors of 1-Bit Booleans},
author = {Jens Oehlschlagel},
year = {2018},
note = {R package version 1.1-14},
url = {https://CRAN.R-project.org/package=bit},
}
@Article{MSnbase,
title = {MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation},
author = {Laurent Gatto and Kathryn Lilley},
journal = {Bioinformatics},
year = {2012},
volume = {28},
pages = {288-289},
}
@Article{mzR1,
author = {{Chambers} and Matthew C. and {Maclean} and {Brendan} and {Burke} and {Robert} and {Amodei} and {Dario} and {Ruderman} and Daniel L. and {Neumann} and {Steffen} and {Gatto} and {Laurent} and {Fischer} and {Bernd} and {Pratt} and {Brian} and {Egertson} and {Jarrett} and {Hoff} and {Katherine} and {Kessner} and {Darren} and {Tasman} and {Natalie} and {Shulman} and {Nicholas} and {Frewen} and {Barbara} and {Baker} and Tahmina A. and {Brusniak} and {Mi-Youn} and {Paulse} and {Christopher} and {Creasy} and {David} and {Flashner} and {Lisa} and {Kani} and {Kian} and {Moulding} and {Chris} and {Seymour} and Sean L. and {Nuwaysir} and Lydia M. and {Lefebvre} and {Brent} and {Kuhlmann} and {Frank} and {Roark} and {Joe} and {Rainer} and {Paape} and {Detlev} and {Suckau} and {Hemenway} and {Tina} and {Huhmer} and {Andreas} and {Langridge} and {James} and {Connolly} and {Brian} and {Chadick} and {Trey} and {Holly} and {Krisztina} and {Eckels} and {Josh} and {Deutsch} and Eric W. and {Moritz} and Robert L. and {Katz} and Jonathan E. and {Agus} and David B. and {MacCoss} and {Michael} and {Tabb} and David L. and {Mallick} and {Parag}},
year = {2012},
journal = {Nat Biotech},
title = {{A cross-platform toolkit for mass spectrometry and proteomics}},
doi = {10.1038/nbt.2377},
pmid = {23051804},
month = {oct},
number = {10},
volume = {30},
pages = {918--920},
url = {http://dx.doi.org/10.1038/nbt.2377},
}
@Article{mzR2,
author = {Lennart Martens and Matthew Chambers and Marc Sturm and Darren Kessner and Fredrik Levander and Jim Shofstahl and Wilfred H Tang and Andreas Rompp and Steffen Neumann and Angel D Pizarro and Luisa Montecchi-Palazzi and Natalie Tasman and Mike Coleman and Florian Reisinger and Puneet Souda and Henning Hermjakob and Pierre-Alain Binz and Eric W Deutsch},
title = {mz{ML} - a {C}ommunity {S}tandard for {M}ass {S}pectrometry {D}ata.},
journal = {{Mol Cell Proteomics}},
year = {2010},
pmid = {20716697},
doi = {10.1074/mcp.R110.000133},
}
@Article{mzR3,
author = {Patrick G A Pedrioli and Jimmy K Eng and Robert Hubley and Mathijs Vogelzang and Eric W Deutsch and Brian Raught and Brian Pratt and Erik Nilsson and Ruth H Angeletti and Rolf Apweiler and Kei Cheung and Catherine E Costello and Henning Hermjakob and Sequin Huang and Randall K Julian and Eugene Kapp and Mark E McComb and Stephen G Oliver and Gilbert Omenn and Norman W Paton and Richard Simpson and Richard Smith and Chris F Taylor and Weimin Zhu and Ruedi Aebersold},
title = {{A} common open representation of mass spectrometry data and its
application to proteomics research.},
journal = {Nat Biotechnol},
year = {2004},
volume = {22},
number = {11},
pages = {{1459--1466}},
pmid = {15529173},
doi = {10.1038/nbt1031},
}
@Article{mzR4,
author = {Andrew Keller and Jimmy Eng and Ning Zhang and Xiao-jun Li and Ruedi Aebersold},
title = {{A} uniform proteomics {MS}/{MS} analysis platform utilizing open {XML} file formats.},
journal = {Mol Syst Biol},
year = {2005},
}
@Article{mzR5,
author = {Darren Kessner and Matt Chambers and Robert Burke and David Agus and Parag Mallick},
title = {{P}roteo{W}izard: open source software for rapid proteomics tools
development.},
journal = {Bioinformatics},
year = {2008},
volume = {24},
number = {21},
pages = {2534--2536},
doi = {10.1093/bioinformatics/btn323},
pmid = {18606607},
}
@Article{plyr,
title = {The Split-Apply-Combine Strategy for Data Analysis},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {1},
pages = {1--29},
url = {http://www.jstatsoft.org/v40/i01/},
}
@Manual{RANN,
title = {RANN: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric},
author = {Sunil Arya and David Mount and Samuel E. Kemp and Gregory Jefferis},
year = {2019},
note = {R package version 2.6.1},
url = {https://CRAN.R-project.org/package=RANN},
}
@Article{MassSpecWavelet,
author = {Pan Du and Warren A. Kibbe and Simon M. Lin},
title = {Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
journal = {Bioinformatics},
year = {2006},
volume = {22},
pages = {2059-2065},
}
@Manual{robustbase1,
title = {robustbase: Basic Robust Statistics},
author = {Martin Maechler and Peter Rousseeuw and Christophe Croux and Valentin Todorov and Andreas Ruckstuhl and Matias Salibian-Barrera and Tobias Verbeke and Manuel Koller and Eduardo L. T. Conceicao and Maria {Anna di Palma}},
year = {2019},
note = {R package version 0.93-5},
url = {http://robustbase.r-forge.r-project.org/},
url = {http://robustbase.r-forge.r-project.org/},
}
@Article{robustbase2,
title = {An Object-Oriented Framework for Robust Multivariate Analysis},
author = {Valentin Todorov and Peter Filzmoser},
journal = {Journal of Statistical Software},
year = {2009},
volume = {32},
number = {3},
pages = {1--47},
url = {http://www.jstatsoft.org/v32/i03/},
}
@Article{Formula,
title = {Extended Model Formulas in {R}: Multiple Parts and Multiple Responses},
author = {Achim Zeileis and Yves Croissant},
journal = {Journal of Statistical Software},
year = {2010},
volume = {34},
number = {1},
pages = {1--13},
doi = {10.18637/jss.v034.i01},
}
@Manual{latticeExtra,
title = {latticeExtra: Extra Graphical Utilities Based on Lattice},
author = {Deepayan Sarkar and Felix Andrews},
year = {2016},
note = {R package version 0.6-28},
url = {https://CRAN.R-project.org/package=latticeExtra},
}
@Manual{acepack,
title = {acepack: ACE and AVAS for Selecting Multiple Regression Transformations},
author = {Phil Spector and Jerome Friedman and Robert Tibshirani and Thomas Lumley and Shawn Garbett and Jonathan Baron},
year = {2016},
note = {R package version 1.4.1},
url = {https://CRAN.R-project.org/package=acepack},
}
@Manual{htmlTable,
title = {htmlTable: Advanced Tables for Markdown/HTML},
author = {Max Gordon and Stephen Gragg and Peter Konings},
year = {2019},
note = {R package version 1.13.2},
url = {https://CRAN.R-project.org/package=htmlTable},
}
@Manual{viridis,
title = {viridis: Default Color Maps from 'matplotlib'},
author = {Simon Garnier},
year = {2018},
note = {R package version 0.5.1},
url = {https://CRAN.R-project.org/package=viridis},
}
@Manual{base64enc,
title = {base64enc: Tools for base64 encoding},
author = {Simon Urbanek},
year = {2015},
note = {R package version 0.1-3},
url = {https://CRAN.R-project.org/package=base64enc},
}
@Manual{labeling,
title = {labeling: Axis Labeling},
author = {Justin Talbot},
year = {2014},
note = {R package version 0.3},
url = {https://CRAN.R-project.org/package=labeling},
}
@Manual{munsell,
title = {munsell: Utilities for Using Munsell Colours},
author = {Charlotte Wickham},
year = {2018},
note = {R package version 0.5.0},
url = {https://CRAN.R-project.org/package=munsell},
}
@Manual{fansi,
title = {fansi: ANSI Control Sequence Aware String Functions},
author = {Brodie Gaslam},
year = {2018},
note = {R package version 0.4.0},
url = {https://CRAN.R-project.org/package=fansi},
}
@Manual{pillar,
title = {pillar: Coloured Formatting for Columns},
author = {Kirill Muller and Hadley Wickham},
year = {2019},
note = {R package version 1.4.2},
url = {https://CRAN.R-project.org/package=pillar},
}
@Manual{biglm,
title = {biglm: bounded memory linear and generalized linear models},
author = {Thomas Lumley},
year = {2013},
note = {R package version 0.9-1},
url = {https://CRAN.R-project.org/package=biglm},
}
@Manual{yaml,
title = {yaml: Methods to Convert R Data to YAML and Back},
author = {Jeremy Stephens and Kirill Simonov and Yihui Xie and Zhuoer Dong and Hadley Wickham and Jeffrey Horner and {reikoch} and Will Beasley and Brendan O'Connor and Gregory R. Warnes},
year = {2018},
note = {R package version 2.2.0},
url = {https://CRAN.R-project.org/package=yaml},
}
@Manual{bitops,
title = {bitops: Bitwise Operations},
author = {S original by Steve Dutky initial R port and extensions by Martin Maechler; revised and modified by Steve Dutky},
year = {2013},
note = {R package version 1.0-6},
url = {https://CRAN.R-project.org/package=bitops},
}
@Manual{lambda.r,
title = {lambda.r: Modeling Data with Functional Programming},
author = {Brian Lee Yung Rowe},
year = {2019},
note = {R package version 1.2.4},
url = {https://CRAN.R-project.org/package=lambda.r},
}
@Manual{futile.options,
title = {futile.options: Futile Options Management},
author = {Brian Lee Yung Rowe},
year = {2018},
note = {R package version 1.0.1},
url = {https://CRAN.R-project.org/package=futile.options},
}
@Manual{clipr,
title = {clipr: Read and Write from the System Clipboard},
author = {Matthew Lincoln},
year = {2019},
note = {R package version 0.7.0},
url = {https://CRAN.R-project.org/package=clipr},
}
@Manual{clisymbols,
title = {clisymbols: Unicode Symbols at the R Prompt},
author = {Gabor Csardi and Sindre Sorhus},
year = {2017},
note = {R package version 1.2.0},
url = {https://CRAN.R-project.org/package=clisymbols},
}
@Manual{gh,
title = {gh: 'GitHub' 'API'},
author = {Jennifer Bryan and Hadley Wickham},
year = {2017},
note = {R package version 1.0.1},
url = {https://CRAN.R-project.org/package=gh},
}
@Manual{rprojroot,
title = {rprojroot: Finding Files in Project Subdirectories},
author = {Kirill Muller},
year = {2018},
note = {R package version 1.3-2},
url = {https://CRAN.R-project.org/package=rprojroot},
}
@Manual{whisker,
title = {whisker: {{mustache}} for R, Logicless Templating},
author = {Edwin {de Jonge}},
year = {2019},
note = {R package version 0.4},
url = {https://CRAN.R-project.org/package=whisker},
}
@Manual{rex,
title = {rex: Friendly Regular Expressions},
author = {Kevin Ushey and Jim Hester and Robert Krzyzanowski},
year = {2017},
note = {R package version 1.1.2},
url = {https://CRAN.R-project.org/package=rex},
}
@Manual{promises,
title = {promises: Abstractions for Promise-Based Asynchronous Programming},
author = {Joe Cheng},
year = {2019},
note = {R package version 1.1.0},
url = {https://CRAN.R-project.org/package=promises},
}
@Manual{mime,
title = {mime: Map Filenames to MIME Types},
author = {Yihui Xie},
year = {2019},
note = {R package version 0.7},
url = {https://CRAN.R-project.org/package=mime},
}
@Manual{openssl,
title = {openssl: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL},
author = {Jeroen Ooms},
year = {2019},
note = {R package version 1.4.1},
url = {https://CRAN.R-project.org/package=openssl},
}
@Manual{prettyunits,
title = {prettyunits: Pretty, Human Readable Formatting of Quantities},
author = {Gabor Csardi},
year = {2015},
note = {R package version 1.0.2},
url = {https://CRAN.R-project.org/package=prettyunits},
}
@Manual{xopen,
title = {xopen: Open System Files, 'URLs', Anything},
author = {Gabor Csardi and Fathi Boudra and Rex Dieter and Kevin Krammer and Jeremy White},
year = {2018},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=xopen},
}
@Manual{brew,
title = {brew: Templating Framework for Report Generation},
author = {Jeffrey Horner},
year = {2011},
note = {R package version 1.0-6},
url = {https://CRAN.R-project.org/package=brew},
}
@Manual{commonmark,
title = {commonmark: High Performance CommonMark and Github Markdown Rendering in R},
author = {Jeroen Ooms},
year = {2018},
note = {R package version 1.7},
url = {https://CRAN.R-project.org/package=commonmark},
}
@Manual{xml2,
title = {xml2: Parse XML},
author = {Hadley Wickham and Jim Hester and Jeroen Ooms},
year = {2019},
note = {R package version 1.2.2},
url = {https://CRAN.R-project.org/package=xml2},
}
@Manual{evaluate,
title = {evaluate: Parsing and Evaluation Tools that Provide More Details than the
Default},
author = {Hadley Wickham and Yihui Xie},
year = {2019},
note = {R package version 0.14},
url = {https://CRAN.R-project.org/package=evaluate},
}
@Manual{praise,
title = {praise: Praise Users},
author = {Gabor Csardi and Sindre Sorhus},
year = {2015},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=praise},
}
@Manual{classInt,
title = {classInt: Choose Univariate Class Intervals},
author = {Roger Bivand},
year = {2019},
note = {R package version 0.4-2},
url = {https://CRAN.R-project.org/package=classInt},
}
@Manual{DBI,
title = {DBI: R Database Interface},
author = {{R Special Interest Group on Databases (R-SIG-DB)} and Hadley Wickham and Kirill Muller},
year = {2018},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=DBI},
}
@Article{units,
title = {Measurement Units in {R}},
author = {Edzer Pebesma and Thomas Mailund and James Hiebert},
year = {2016},
journal = {R Journal},
doi = {10.32614/RJ-2016-061},
pages = {486--494},
volume = {8},
number = {2},
}
@Manual{gdata,
title = {gdata: Various R Programming Tools for Data Manipulation},
author = {Gregory R. Warnes and Ben Bolker and Gregor Gorjanc and Gabor Grothendieck and Ales Korosec and Thomas Lumley and Don MacQueen and Arni Magnusson and Jim Rogers and others},
year = {2017},
note = {R package version 2.18.0},
url = {https://CRAN.R-project.org/package=gdata},
}
@Manual{highr,
title = {highr: Syntax Highlighting for R Source Code},
author = {Yixuan Qiu and Yihui Xie},
year = {2019},
note = {R package version 0.8},
url = {https://CRAN.R-project.org/package=highr},
}
@Manual{markdown,
title = {markdown: Render Markdown with the C Library 'Sundown'},
author = {JJ Allaire and Jeffrey Horner and Yihui Xie and Vicent Marti and Natacha Porte},
year = {2019},
note = {R package version 1.1},
url = {https://CRAN.R-project.org/package=markdown},
}
@Manual{xfun,
title = {xfun: Miscellaneous Functions by 'Yihui Xie'},
author = {Yihui Xie},
year = {2019},
note = {R package version 0.10},
url = {https://CRAN.R-project.org/package=xfun},
}
@Manual{httpuv,
title = {httpuv: HTTP and WebSocket Server Library},
author = {Joe Cheng and Hector Corrada Bravo and Jeroen Ooms and Winston Chang},
year = {2019},
note = {R package version 1.5.2},
url = {https://CRAN.R-project.org/package=httpuv},
}
@Manual{xtable,
title = {xtable: Export Tables to LaTeX or HTML},
author = {David B. Dahl and David Scott and Charles Roosen and Arni Magnusson and Jonathan Swinton},
year = {2019},
note = {R package version 1.8-4},
url = {https://CRAN.R-project.org/package=xtable},
}
@Manual{sourcetools,
title = {sourcetools: Tools for Reading, Tokenizing and Parsing R Code},
author = {Kevin Ushey},
year = {2018},
note = {R package version 0.1.7},
url = {https://CRAN.R-project.org/package=sourcetools},
}
@Manual{later,
title = {later: Utilities for Scheduling Functions to Execute Later with Event
Loops},
author = {Joe Cheng and Winston Chang},
year = {2019},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=later},
}
@Manual{fastmap,
title = {fastmap: Fast Implementation of a Key-Value Store},
author = {Winston Chang},
year = {2019},
note = {R package version 1.0.1},
url = {https://CRAN.R-project.org/package=fastmap},
}
@Manual{miniUI,
title = {miniUI: Shiny UI Widgets for Small Screens},
author = {Joe Cheng},
year = {2018},
note = {R package version 0.1.1.1},
url = {https://CRAN.R-project.org/package=miniUI},
}
@Manual{webshot,
title = {webshot: Take Screenshots of Web Pages},
author = {Winston Chang},
year = {2018},
note = {R package version 0.5.1},
url = {https://CRAN.R-project.org/package=webshot},
}
@Manual{bit64,
title = {bit64: A S3 Class for Vectors of 64bit Integers},
author = {Jens Oehlschlagel},
year = {2017},
note = {R package version 0.9-7},
url = {https://CRAN.R-project.org/package=bit64},
}
@Manual{blob,
title = {blob: A Simple S3 Class for Representing Vectors of Binary Data
('BLOBS')},
author = {Hadley Wickham},
year = {2019},
note = {R package version 1.2.0},
url = {https://CRAN.R-project.org/package=blob},
}
@Manual{dbplyr,
title = {dbplyr: A 'dplyr' Back End for Databases},
author = {Hadley Wickham and Edgar Ruiz},
year = {2019},
note = {R package version 1.4.2},
url = {https://CRAN.R-project.org/package=dbplyr},
}
@Article{Biobase,
author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. MacDonald and V. Obenchain and A. K. {Ole's} and H. {Pag`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and M. Morgan},
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{xcms1,
author = {{Smith} and {C.A.} and {Want} and {E.J.} and {O'Maille} and {G.} and {Abagyan,R.} and {Siuzdak} and {G.}},
title = {XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification},
journal = {Analytical Chemistry},
year = {2006},
volume = {78},
pages = {779--787},
}
@Article{xcms2,
author = {Ralf Tautenhahn and Christoph Boettcher and Steffen Neumann},
title = {Highly sensitive feature detection for high resolution LC/MS},
journal = {BMC Bioinformatics},
year = {2008},
volume = {9},
pages = {504},
}
@Article{xcms3,
author = {H. Paul Benton and Elizabeth J. Want and Timothy M. D. Ebbels},
title = {Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data},
journal = {BIOINFORMATICS},
year = {2010},
volume = {26},
pages = {2488},
}
@Manual{RBGL,
title = {RBGL: An interface to the BOOST graph library},
author = {Vince Carey and Li Long and R. Gentleman},
year = {2019},
note = {R package version 1.60.0},
url = {http://www.bioconductor.org},
}
@Manual{graph,
title = {graph: graph: A package to handle graph data structures},
author = {R. Gentleman and Elizabeth Whalen and W. Huber and S. Falcon},
year = {2019},
note = {R package version 1.62.0},
}
@Manual{Hmisc,
title = {Hmisc: Harrell Miscellaneous},
author = {Frank E {Harrell Jr} and with contributions from Charles Dupont and many others.},
year = {2019},
note = {R package version 4.3-0},
url = {https://CRAN.R-project.org/package=Hmisc},
}
@Manual{remotes,
title = {remotes: R Package Installation from Remote Repositories, Including
'GitHub'},
author = {Jim Hester and Gabor Csardi and Hadley Wickham and Winston Chang and Martin Morgan and Dan Tenenbaum},
year = {2019},
note = {R package version 2.1.0},
url = {https://CRAN.R-project.org/package=remotes},
}
@Manual{magrittr,
title = {magrittr: A Forward-Pipe Operator for R},
author = {Stefan Milton Bache and Hadley Wickham},
year = {2014},
note = {R package version 1.5},
url = {https://CRAN.R-project.org/package=magrittr},
}
@Manual{rlang,
title = {rlang: Functions for Base Types and Core R and 'Tidyverse' Features},
author = {Lionel Henry and Hadley Wickham},
year = {2019},
note = {R package version 0.4.0},
url = {https://CRAN.R-project.org/package=rlang},
}
@Manual{curl,
title = {curl: A Modern and Flexible Web Client for R},
author = {Jeroen Ooms},
year = {2019},
note = {R package version 4.2},
url = {https://CRAN.R-project.org/package=curl},
}
@Manual{digest,
title = {digest: Create Compact Hash Digests of R Objects},
author = {Dirk Eddelbuettel with contributions by Antoine Lucas and Jarek Tuszynski and Henrik Bengtsson and Simon Urbanek and Mario Frasca and Bryan Lewis and Murray Stokely and Hannes Muehleisen and Duncan Murdoch and Jim Hester and Wush Wu and Qiang Kou and Thierry Onkelinx and Michel Lang and Viliam Simko and Kurt Hornik and Radford Neal and Kendon Bell and and Matthew {de Queljoe.}},
year = {2019},
note = {R package version 0.6.21},
url = {https://CRAN.R-project.org/package=digest},
}
@Manual{lazyeval,
title = {lazyeval: Lazy (Non-Standard) Evaluation},
author = {Hadley Wickham},
year = {2019},
note = {R package version 0.2.2},
url = {https://CRAN.R-project.org/package=lazyeval},
}
@Article{reshape2,
title = {Reshaping Data with the {reshape} Package},
author = {Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2007},
volume = {21},
number = {12},
pages = {1--20},
url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{scales,
title = {scales: Scale Functions for Visualization},
author = {Hadley Wickham},
year = {2018},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=scales},
}
@Manual{tibble,
title = {tibble: Simple Data Frames},
author = {Kirill Muller and Hadley Wickham},
year = {2019},
note = {R package version 2.1.3},
url = {https://CRAN.R-project.org/package=tibble},
}
@Manual{viridisLite,
title = {viridisLite: Default Color Maps from 'matplotlib' (Lite Version)},
author = {Simon Garnier},
year = {2018},
note = {R package version 0.3.0},
url = {https://CRAN.R-project.org/package=viridisLite},
}
@Manual{withr,
title = {withr: Run Code 'With' Temporarily Modified Global State},
author = {Jim Hester and Kirill Muller and Kevin Ushey and Hadley Wickham and Winston Chang},
year = {2018},
note = {R package version 2.1.2},
url = {https://CRAN.R-project.org/package=withr},
}
@Article{jsonlite,
title = {The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects},
author = {Jeroen Ooms},
journal = {arXiv:1403.2805 [stat.CO]},
year = {2014},
url = {https://arxiv.org/abs/1403.2805},
}
@Manual{assertthat,
title = {assertthat: Easy Pre and Post Assertions},
author = {Hadley Wickham},
year = {2019},
note = {R package version 0.2.1},
url = {https://CRAN.R-project.org/package=assertthat},
}
@Manual{glue,
title = {glue: Interpreted String Literals},
author = {Jim Hester},
year = {2019},
note = {R package version 1.3.1},
url = {https://CRAN.R-project.org/package=glue},
}
@Manual{pkgconfig,
title = {pkgconfig: Private Configuration for 'R' Packages},
author = {Gabor Csardi},
year = {2019},
note = {R package version 2.0.3},
url = {https://CRAN.R-project.org/package=pkgconfig},
}
@Manual{R6,
title = {R6: Encapsulated Classes with Reference Semantics},
author = {Winston Chang},
year = {2019},
note = {R package version 2.4.0},
url = {https://CRAN.R-project.org/package=R6},
}
@Manual{tidyselect,
title = {tidyselect: Select from a Set of Strings},
author = {Lionel Henry and Hadley Wickham},
year = {2018},
note = {R package version 0.2.5},
url = {https://CRAN.R-project.org/package=tidyselect},
}
@Manual{BH,
title = {BH: Boost C++ Header Files},
author = {Dirk Eddelbuettel and John W. Emerson and Michael J. Kane},
year = {2019},
note = {R package version 1.69.0-1},
url = {https://CRAN.R-project.org/package=BH},
}
@Manual{plogr,
title = {plogr: The 'plog' C++ Logging Library},
author = {Kirill Muller},
year = {2018},
note = {R package version 0.2.0},
url = {https://CRAN.R-project.org/package=plogr},
}
@Manual{stringi,
title = {R package stringi: Character string processing facilities},
author = {Marek Gagolewski},
year = {2019},
url = {http://www.gagolewski.com/software/stringi/},
}
@Manual{zlibbioc,
title = {zlibbioc: An R packaged zlib-1.2.5},
author = {Martin Morgan},
year = {2019},
note = {R package version 1.30.0},
url = {http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html},
}
@Manual{irlba,
title = {irlba: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices},
author = {Jim Baglama and Lothar Reichel and B. W. Lewis},
year = {2019},
note = {R package version 2.3.3},
url = {https://CRAN.R-project.org/package=irlba},
}
@Manual{matter,
title = {matter: A framework for rapid prototyping with binary data on disk},
author = {Kylie A. Bemis},
year = {2019},
note = {R package version 1.10.0},
url = {https://github.com/kuwisdelu/matter},
}
@Article{mclust,
title = {{mclust} 5: clustering, classification and density estimation using {G}aussian finite mixture models},
author = {Luca Scrucca and Michael Fop and Thomas Brendan Murphy and Adrian E. Raftery},
journal = {The {R} Journal},
year = {2016},
volume = {8},
number = {1},
pages = {205--233},
url = {https://journal.r-project.org/archive/2016-1/scrucca-fop-murphy-etal.pdf},
}
@Manual{signal,
title = {{signal}: Signal processing},
author = {{signal developers}},
year = {2014},
url = {http://r-forge.r-project.org/projects/signal/},
}
@Article{sp1,
author = {Edzer J. Pebesma and Roger S. Bivand},
title = {Classes and methods for spatial data in {R}},
journal = {R News},
year = {2005},
volume = {5},
number = {2},
pages = {9--13},
month = {November},
url = {https://CRAN.R-project.org/doc/Rnews/},
}
@Book{sp2,
author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gomez-Rubio},
title = {Applied spatial data analysis with {R}, Second edition},
year = {2013},
publisher = {Springer, NY},
url = {http://www.asdar-book.org/},