book.bib

@article{deelen15,
  title = {Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels.},
  author = {Patrick Deelen et al.},
  year = {2015},
  journal = {Genome Medicine},
  volume = {7},
  number = {30},
}
@article{jiang14,
  title = {RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene That Modulates Cytokine Function in Airway Smooth Muscle Cells},
  author = {Himes BE, Jiang X, Wagner P, et al.},
  year = {2014},
  journal = {PLoS One},
  volume = {9},
  number = {6}
}
@article{law14,
  title= {voom: precision weights unlock linear model analysis tools for RNA-seq read counts},
  author = {Charity W Law, Yunshun Chen, Wei Shi and Gordon K Smyth},
  year = {2014},
  journal = {Genome Biology},
  volume = {15},
  number = {R29}
}
@Manual{R-AnnotationDbi,
  title = {AnnotationDbi: Annotation Database Interface},
  author = {Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li},
  year = {2017},
  note = {R package version 1.40.0},
}
@Manual{R-base,
  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{R-Biobase,
  title = {Biobase: Base functions for Bioconductor},
  author = {R. Gentleman and V. Carey and M. Morgan and S. Falcon},
  year = {2017},
  note = {R package version 2.38.0},
}
@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions for Bioconductor},
  author = {The Bioconductor Dev Team},
  year = {2017},
  note = {R package version 0.24.0},
}
@Manual{R-biomaRt,
  title = {biomaRt: Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase
and Gramene)},
  author = {Steffen Durinck and Wolfgang Huber},
  year = {2018},
  note = {R package version 2.34.2},
}
@Manual{R-bitops,
  title = {bitops: Bitwise Operations},
  author = {Steve Dutky and Martin Maechler},
  year = {2013},
  note = {R package version 1.0-6},
  url = {https://CRAN.R-project.org/package=bitops},
}
@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2017},
  note = {R package version 0.5.16},
  url = {https://github.com/rstudio/bookdown},
}
@Manual{R-DelayedArray,
  title = {DelayedArray: Delayed operations on array-like objects},
  author = {Hervé Pagès},
  year = {2017},
  note = {R package version 0.4.1},
}
@Manual{R-DESeq2,
  title = {DESeq2: Differential gene expression analysis based on the negative
binomial distribution},
  author = {Michael Love and Simon Anders and Wolfgang Huber},
  year = {2017},
  note = {R package version 1.18.1},
  url = {https://github.com/mikelove/DESeq2},
}
@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain Francois and Lionel Henry and Kirill Müller},
  year = {2017},
  note = {R package version 0.7.4},
  url = {https://CRAN.R-project.org/package=dplyr},
}
@Manual{R-edgeR,
  title = {edgeR: Empirical Analysis of Digital Gene Expression Data in R},
  author = {Yunshun Chen and Aaron Lun and Davis McCarthy and Xiaobei Zhou and Mark Robinson and Gordon Smyth},
  year = {2018},
  note = {R package version 3.20.7},
  url = {http://bioinf.wehi.edu.au/edgeR},
}
@Manual{R-futile.logger,
  title = {futile.logger: A Logging Utility for R},
  author = {Brian Lee Yung Rowe},
  year = {2016},
  note = {R package version 1.4.3},
  url = {https://CRAN.R-project.org/package=futile.logger},
}
@Manual{R-GenomeInfoDb,
  title = {GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname'
identifiers},
  author = {Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès},
  year = {2017},
  note = {R package version 1.14.0},
}
@Manual{R-GenomicRanges,
  title = {GenomicRanges: Representation and manipulation of genomic intervals and
variables defined along a genome},
  author = {P. Aboyoun and H. Pagès and M. Lawrence},
  year = {2017},
  note = {R package version 1.30.1},
}
@Manual{R-GEOmetadb,
  title = {GEOmetadb: A compilation of metadata from NCBI GEO},
  author = {Jack Zhu and Sean Davis},
  year = {2017},
  note = {R package version 1.40.0},
  url = {http://gbnci.abcc.ncifcrf.gov/geo/},
}
@Manual{R-GEOquery,
  title = {GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)},
  author = {Sean Davis},
  year = {2017},
  note = {R package version 2.46.13},
  url = {https://github.com/seandavi/GEOquery},
}
@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang},
  year = {2016},
  note = {R package version 2.2.1},
  url = {https://CRAN.R-project.org/package=ggplot2},
}
@Manual{R-ggrepel,
  title = {ggrepel: Repulsive Text and Label Geoms for 'ggplot2'},
  author = {Kamil Slowikowski},
  year = {2017},
  note = {R package version 0.7.0},
  url = {https://CRAN.R-project.org/package=ggrepel},
}
@Manual{R-gplots,
  title = {gplots: Various R Programming Tools for Plotting Data},
  author = {Gregory R. Warnes and Ben Bolker and Lodewijk Bonebakker and Robert Gentleman and Wolfgang Huber Andy Liaw and Thomas Lumley and Martin Maechler and Arni Magnusson and Steffen Moeller and Marc Schwartz and Bill Venables},
  year = {2016},
  note = {R package version 3.0.1},
  url = {https://CRAN.R-project.org/package=gplots},
}
@Manual{R-graph,
  title = {graph: A package to handle graph data structures},
  author = {R. Gentleman and Elizabeth Whalen and W. Huber and S. Falcon},
  year = {2017},
  note = {R package version 1.56.0},
}
@Manual{R-IRanges,
  title = {IRanges: Infrastructure for manipulating intervals on sequences},
  author = {H. Pagès and P. Aboyoun and M. Lawrence},
  year = {2017},
  note = {R package version 2.12.0},
}
@Manual{R-KEGGgraph,
  title = {KEGGgraph: A graph approach to KEGG PATHWAY in R and
Bioconductor},
  author = {Jitao David Zhang and with inputs from Paul Shannon},
  year = {2017},
  note = {R package version 1.38.0},
  url = {http://www.nextbiomotif.com},
}
@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2017},
  note = {R package version 1.18},
  url = {https://CRAN.R-project.org/package=knitr},
}
@Manual{R-limma,
  title = {limma: Linear Models for Microarray Data},
  author = {Gordon Smyth and Yifang Hu and Matthew Ritchie and Jeremy Silver and James Wettenhall and Davis McCarthy and Di Wu and Wei Shi and Belinda Phipson and Aaron Lun and Natalie Thorne and Alicia Oshlack and Carolyn {de Graaf} and Yunshun Chen and Mette Langaas and Egil Ferkingstad and Marcus Davy and Francois Pepin and Dongseok Choi},
  year = {2017},
  note = {R package version 3.34.5},
  url = {http://bioinf.wehi.edu.au/limma},
}
@Manual{R-matrixStats,
  title = {matrixStats: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)},
  author = {Henrik Bengtsson},
  year = {2017},
  note = {R package version 0.52.2},
  url = {https://CRAN.R-project.org/package=matrixStats},
}
@Manual{R-org.Mm.eg.db,
  title = {org.Mm.eg.db: Genome wide annotation for Mouse},
  author = {Marc Carlson},
  year = {2017},
  note = {R package version 3.5.0},
}
@Manual{R-pander,
  title = {pander: An R 'Pandoc' Writer},
  author = {Gergely Daróczi and Roman Tsegelskyi},
  year = {2017},
  note = {R package version 0.6.1},
  url = {https://CRAN.R-project.org/package=pander},
}
@Manual{R-pheatmap,
  title = {pheatmap: Pretty Heatmaps},
  author = {Raivo Kolde},
  year = {2015},
  note = {R package version 1.0.8},
  url = {https://CRAN.R-project.org/package=pheatmap},
}
@Manual{R-png,
  title = {png: Read and write PNG images},
  author = {Simon Urbanek},
  year = {2013},
  note = {R package version 0.1-7},
  url = {https://CRAN.R-project.org/package=png},
}
@Manual{R-PoiClaClu,
  title = {PoiClaClu: Classification and clustering of sequencing data based on a
Poisson model},
  author = {Daniela Witten},
  year = {2013},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=PoiClaClu},
}
@Manual{R-RCurl,
  title = {RCurl: General Network (HTTP/FTP/...) Client Interface for R},
  author = {Duncan {Temple Lang} and the CRAN team},
  year = {2018},
  note = {R package version 1.95-4.10},
  url = {https://CRAN.R-project.org/package=RCurl},
}
@Manual{R-rmarkdown,
  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},
  year = {2017},
  note = {R package version 1.8},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}
@Manual{R-RSQLite,
  title = {RSQLite: 'SQLite' Interface for R},
  author = {Kirill Müller and Hadley Wickham and David A. James and Seth Falcon},
  year = {2017},
  note = {R package version 2.0},
  url = {https://CRAN.R-project.org/package=RSQLite},
}
@Manual{R-S4Vectors,
  title = {S4Vectors: S4 implementation of vector-like and list-like objects},
  author = {H. Pagès and M. Lawrence and P. Aboyoun},
  year = {2017},
  note = {R package version 0.16.0},
}
@Manual{R-SPIA,
  title = {SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence
of pathway over-representation and unusual signaling
perturbations},
  author = {Adi Laurentiu Tarca and Purvesh Kathri and Sorin Draghici},
  year = {2013},
  note = {R package version 2.30.0},
  url = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1},
}
@Manual{R-SRAdb,
  title = {SRAdb: A compilation of metadata from NCBI SRA and tools},
  author = {Jack Zhu and Sean Davis},
  year = {2017},
  note = {R package version 1.40.0},
  url = {http://gbnci.abcc.ncifcrf.gov/sra/},
}
@Manual{R-SummarizedExperiment,
  title = {SummarizedExperiment: SummarizedExperiment container},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
  year = {2017},
  note = {R package version 1.8.1},
}
@Manual{R-VennDiagram,
  title = {VennDiagram: Generate High-Resolution Venn and Euler Plots},
  author = {Hanbo Chen},
  year = {2017},
  note = {R package version 1.6.18},
  url = {https://CRAN.R-project.org/package=VennDiagram},
}