This workshop aims to describe the SPEAQeasy RNA-seq processing pipeline, show how to use it, and then illustrate how the results can be analyzed using Bioconductor R packages for differential expression analyses.
SPEAQeasy is a Nextflow-based Scalable RNA-seq processing Pipeline for Expression Analysis and Quantification that produces R objects ready for analysis with Bioconductor tools. Partipants will become familiar with SPEAQeasy set-up, execution on real data, and practice configuring some common settings. We will walk through a complete differential expression analysis, utilizing popular packages such as limma, edgeR, and clusterProfiler.
Citation
Below is the citation output from using citation('SPEAQeasyWorkshop2020') in R. Please run this yourself to check for any updates on how to cite SPEAQeasyWorkshop2020.
print(citation("SPEAQeasyWorkshop2020"), bibtex = TRUE)
#>
#> Eagles NJ, Stolz JM, Collado-Torres L (2020). _EuroBioc2020 SPEAQeasy
#> workshop_. doi: 10.18129/B9.bioc.SPEAQeasyWorkshop2020 (URL:
#> https://doi.org/10.18129/B9.bioc.SPEAQeasyWorkshop2020),
#> https://github.com/LieberInstitute/SPEAQeasyWorkshop2020 - R package
#> version 0.99.0, <URL:
#> http://www.bioconductor.org/packages/SPEAQeasyWorkshop2020>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {EuroBioc2020 SPEAQeasy workshop},
#> author = {Nicholas J. Eagles and Joshua M. Stolz and Leonardo Collado-Torres},
#> year = {2020},
#> url = {http://www.bioconductor.org/packages/SPEAQeasyWorkshop2020},
#> note = {https://github.com/LieberInstitute/SPEAQeasyWorkshop2020 - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.SPEAQeasyWorkshop2020},
#> }
#>
#> Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN,
#> Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE,
#> Collado-Torres L (2020). "SPEAQeasy: a Scalable Pipeline for Expression
#> Analysis and Quantification for R/Bioconductor-powered RNA-seq
#> analyses." _bioRxiv_. doi: 10.1101/2020.12.11.386789 (URL:
#> https://doi.org/10.1101/2020.12.11.386789), <URL:
#> https://www.biorxiv.org/content/10.1101/2020.12.11.386789v1>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses},
#> author = {Nicholas J. Eagles and Emily E. Burke and Jacob Leonard and Brianna K. Barry and Joshua M. Stolz and Louise Huuki and BaDoi N. Phan and Violeta Larrios Serrato and Everardo Gutiérrez-Millán and Israel Aguilar-Ordoñez and Andrew E. Jaffe and Leonardo Collado-Torres},
#> year = {2020},
#> journal = {bioRxiv},
#> doi = {10.1101/2020.12.11.386789},
#> url = {https://www.biorxiv.org/content/10.1101/2020.12.11.386789v1},
#> }Please note that the SPEAQeasyWorkshop2020 was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
Code of Conduct
Please note that the SPEAQeasyWorkshop2020 project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Development tools
- Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
- Code coverage assessment is possible thanks to codecov and covr.
- The documentation website is automatically updated thanks to pkgdown.
- The code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev directory.
This package was developed using biocthis.
