References

The analyses were made possible thanks to:

R (Fu, Frazee, Collado-Torres, Jaffe, et al., 2019)
ballgown (Waldron, L, Ogino, Shuji, Hoshida, Yujin, Shima, Kaori, et al., 2012)
BiocParallel (R Core Team, 2019)
BiocStyle (Alexa and Rahnenfuhrer, 2019)
coop (Allaire, Xie, McPherson, Luraschi, et al., 2019)
derfinder (Bache and Wickham, 2014)
devtools (Bengtsson, 2018)
downloader (Boettiger, 2017)
dplyr (Carlson, 2019)
edgeR (Chang, 2015)
ffpe (Collado-Torres, Nellore, Frazee, Wilks, et al., 2017)
IHW
knitcitations (Collado-Torres, Nellore, Kammers, Ellis, et al., 2019)
magrittr (Schmidt, 2019)
matrixStats (Ellis, Collado-Torres, Jaffe, and Leek, 2018)
org.Hs.eg.db (Frazee, Langmead, and Leek, 2011)
qvalue (Frazee, 2018)
recount
readr (Robinson, McCarthy, and Smyth, 2010)
rmarkdown
RSkittleBrewer (Wickham, Hester, and Francois, 2018)
stringr (Wickham, Hester, and Chang, 2019)
SummarizedExperiment (Wickham, François, Henry, and Müller, 2019)
topGO (Wickham, 2019)
limma (Xie, Allaire, and Grolemund, 2018)

[1] A. Alexa and J. Rahnenfuhrer. topGO: Enrichment Analysis for Gene Ontology. R package version 2.36.0. 2019.

[1] J. Allaire, Y. Xie, J. McPherson, J. Luraschi, et al. rmarkdown: Dynamic Documents for R. R package version 1.15. 2019. URL: https://github.com/rstudio/rmarkdown.

[1] S. M. Bache and H. Wickham. magrittr: A Forward-Pipe Operator for R. R package version 1.5. 2014. URL: https://CRAN.R-project.org/package=magrittr.

[1] H. Bengtsson. matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors). R package version 0.54.0. 2018. URL: https://CRAN.R-project.org/package=matrixStats.

[1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations.

[1] M. Carlson. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.8.2. 2019.

[1] W. Chang. downloader: Download Files over HTTP and HTTPS. R package version 0.4. 2015. URL: https://CRAN.R-project.org/package=downloader.

[1] L. Collado-Torres, A. Nellore, K. Kammers, S. E. Ellis, et al. Explore and download data from the recount project. https://github.com/leekgroup/recount - R package version 1.10.8. 2019. DOI: 10.18129/B9.bioc.recount. URL: http://www.bioconductor.org/packages/recount.

[1] A. Frazee. RSkittleBrewer: Fun with R Colors. R package version 1.1. 2018. URL: https://github.com/alyssafrazee/RSkittleBrewer.

[1] J. Fu, A. C. Frazee, L. Collado-Torres, A. E. Jaffe, et al. ballgown: Flexible, isoform-level differential expression analysis. R package version 2.16.0. 2019.

[1] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2019. URL: https://www.R-project.org/.

[1] D. Schmidt. Co-Operation: Fast Correlation, Covariance, and Cosine Similarity. R package version 0.6-2. 2019. URL: https://cran.r-project.org/package=coop.

[1] H. Wickham. stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0. 2019. URL: https://CRAN.R-project.org/package=stringr.

[1] H. Wickham, R. François, L. Henry, and K. Müller. dplyr: A Grammar of Data Manipulation. R package version 0.8.3. 2019. URL: https://CRAN.R-project.org/package=dplyr.

[1] H. Wickham, J. Hester, and W. Chang. devtools: Tools to Make Developing R Packages Easier. R package version 2.1.0. 2019. URL: https://CRAN.R-project.org/package=devtools.

[1] H. Wickham, J. Hester, and R. Francois. readr: Read Rectangular Text Data. R package version 1.3.1. 2018. URL: https://CRAN.R-project.org/package=readr.

[1] Y. Xie, J. Allaire, and G. Grolemund. R Markdown: The Definitive Guide. ISBN 9781138359338. Boca Raton, Florida: Chapman and Hall/CRC, 2018. URL: https://bookdown.org/yihui/rmarkdown.