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@Manual{2019language,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2019},
url = {https://www.R-project.org/},
}
@Manual{allaire2019rmarkdown,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
year = {2019},
note = {R package version 1.12},
url = {https://rmarkdown.rstudio.com},
}
@Article{Bao_2014,
doi = {10.1101/gr.165126.113},
url = {https://doi.org/10.1101/gr.165126.113},
year = {2014},
month = {aug},
publisher = {Cold Spring Harbor Laboratory},
volume = {24},
number = {11},
pages = {1765--1773},
author = {Zhao-Shi Bao and Hui-Min Chen and Ming-Yu Yang and Chuan-Bao Zhang and Kai Yu and Wan-Lu Ye and Bo-Qiang Hu and Wei Yan and Wei Zhang and Johnny Akers and Valya Ramakrishnan and Jie Li and Bob Carter and Yan-Wei Liu and Hui-Min Hu and Zheng Wang and Ming-Yang Li and Kun Yao and Xiao-Guang Qiu and Chun-Sheng Kang and Yong-Ping You and Xiao-Long Fan and Wei Sonya Song and Rui-Qiang Li and Xiao-Dong Su and Clark C. Chen and Tao Jiang},
title = {{RNA}-seq of 272 gliomas revealed a novel, {recurrentPTPRZ}1-{METfusion} transcript in secondary glioblastomas},
journal = {Genome Research},
}
@Article{Bernstein_2017,
doi = {10.1093/bioinformatics/btx334},
url = {https://doi.org/10.1093/bioinformatics/btx334},
year = {2017},
month = {may},
publisher = {Oxford University Press ({OUP})},
volume = {33},
number = {18},
pages = {2914--2923},
author = {Matthew N Bernstein and AnHai Doan and Colin N Dewey},
editor = {Jonathan Wren},
title = {{MetaSRA}: normalized human sample-specific metadata for the Sequence Read Archive},
journal = {Bioinformatics},
}
@Manual{boettiger2017knitcitations,
title = {knitcitations: Citations for 'Knitr' Markdown Files},
author = {Carl Boettiger},
year = {2017},
note = {R package version 1.0.8},
url = {https://CRAN.R-project.org/package=knitcitations},
}
@Manual{chang2015downloader,
title = {downloader: Download Files over HTTP and HTTPS},
author = {Winston Chang},
year = {2015},
note = {R package version 0.4},
url = {https://CRAN.R-project.org/package=downloader},
}
@Article{colladotorres2017reproducible,
title = {Reproducible RNA-seq analysis using recount2},
author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
year = {2017},
journal = {Nature Biotechnology},
doi = {10.1038/nbt.3838},
url = {http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html},
}
@Manual{colladotorres2018shinycsv,
title = {shinycsv: Explore a table interactively in a shiny application},
author = {Leonardo Collado-Torres and Stephen Semick and Andrew E. Jaffe},
year = {2018},
note = {R package version 0.99.8},
url = {https://github.com/LieberInstitute/shinycsv},
}
@Manual{csrdi2018sessioninfo,
title = {sessioninfo: R Session Information},
author = {G{\a'a}bor Cs{\a'a}rdi and R core and Hadley Wickham and Winston Chang and Robert M Flight and Kirill M{\"u}ller and Jim Hester},
year = {2018},
note = {R package version 1.1.1},
url = {https://CRAN.R-project.org/package=sessioninfo},
}
@Article{ellis2018improving,
title = {Improving the value of public RNA-seq expression data by phenotype prediction},
author = {Shannon E. Ellis and Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
year = {2018},
journal = {Nucl. Acids Res.},
doi = {10.1093/nar/gky102},
url = {https://doi.org/10.1093/nar/gky102},
}
@Article{Ferreira_2018,
doi = {10.1038/s41467-017-02772-x},
url = {https://doi.org/10.1038/s41467-017-02772-x},
year = {2018},
month = {feb},
publisher = {Springer Nature},
volume = {9},
number = {1},
author = {Pedro G. Ferreira and Manuel Mu{\~n}oz-Aguirre and Ferran Reverter and Caio P. S{\a'a} Godinho and Abel Sousa and Alicia Amadoz and Reza Sodaei and Marta R. Hidalgo and Dmitri Pervouchine and Jose Carbonell-Caballero and Ramil Nurtdinov and Alessandra Breschi and Raziel Amador and Patr\'\icia Oliveira and Cankut {\c C}ubuk and Jo{\~a}o Curado and Fran{\c c}ois Aguet and Carla Oliveira and Joaquin Dopazo and Michael Sammeth and Kristin G. Ardlie and Roderic Gui {\a'o}},
title = {The effects of death and post-mortem cold ischemia on human tissue transcriptomes},
journal = {Nature Communications},
}
@Manual{ole2018biocstyle,
title = {BiocStyle: Standard styles for vignettes and other Bioconductor documents},
author = {Andrzej Ole{\a's} and Martin Morgan and Wolfgang Huber},
year = {2018},
note = {R package version 2.10.0},
url = {https://github.com/Bioconductor/BiocStyle},
}
@Article{Whetzel_2011,
doi = {10.1093/nar/gkr469},
url = {https://doi.org/10.1093/nar/gkr469},
year = {2011},
month = {jun},
publisher = {Oxford University Press ({OUP})},
volume = {39},
number = {suppl},
pages = {W541--W545},
author = {P. L. Whetzel and N. F. Noy and N. H. Shah and P. R. Alexander and C. Nyulas and T. Tudorache and M. A. Musen},
title = {{BioPortal}: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications},
journal = {Nucleic Acids Research},
}
@Manual{wickham2017tidyverse,
title = {tidyverse: Easily Install and Load the 'Tidyverse'},
author = {Hadley Wickham},
year = {2017},
note = {R package version 1.2.1},
url = {https://CRAN.R-project.org/package=tidyverse},
}
@Manual{wickham2019devtools,
title = {devtools: Tools to Make Developing R Packages Easier},
author = {Hadley Wickham and Jim Hester and Winston Chang},
year = {2019},
note = {R package version 2.0.2},
url = {https://CRAN.R-project.org/package=devtools},
}
@InCollection{xie2014knitr,
booktitle = {Implementing Reproducible Computational Research},
editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
year = {2014},
note = {ISBN 978-1466561595},
url = {http://www.crcpress.com/product/isbn/9781466561595},
}
@Book{xie2018markdown,
title = {R Markdown: The Definitive Guide},
author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2018},
note = {ISBN 9781138359338},
url = {https://bookdown.org/yihui/rmarkdown},
}
@Manual{xie2018wrapper,
title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
author = {Yihui Xie and Joe Cheng and Xianying Tan},
year = {2018},
note = {R package version 0.5},
url = {https://CRAN.R-project.org/package=DT},
}