The goal of SPEAQeasyWorkshop2023 is to describe how outputs from the SPEAQeasy pipeline enable differential-expression analyses powered by Bioconductor packages like limma, edgeR, and clusterProfiler.
Installation instructions
Get the latest stable R release from CRAN. Then install SPEAQeasyWorkshop2023 from Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("SPEAQeasyWorkshop2023")And the development version from GitHub with:
BiocManager::install("LieberInstitute/SPEAQeasyWorkshop2023")Citation
Below is the citation output from using citation('SPEAQeasyWorkshop2023') in R. Please run this yourself to check for any updates on how to cite SPEAQeasyWorkshop2023.
print(citation("SPEAQeasyWorkshop2023"), bibtex = TRUE)
#>
#> Gomez-Padilla D, Garcia-Flores R, Eagles NJ (2023). _Bioc2023 SPEAQeasy
#> workshop_. doi: 10.18129/B9.bioc.SPEAQeasyWorkshop2023 (URL:
#> https://doi.org/10.18129/B9.bioc.SPEAQeasyWorkshop2023),
#> https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/SPEAQeasyWorkshop2023
#> - R package version 0.99.0, <URL:
#> http://www.bioconductor.org/packages/SPEAQeasyWorkshop2023>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Bioc2023 SPEAQeasy workshop},
#> author = {Daianna Gomez-Padilla and Renee Garcia-Flores and Nicholas J. Eagles},
#> year = {2023},
#> url = {http://www.bioconductor.org/packages/SPEAQeasyWorkshop2023},
#> note = {https://github.com/LieberInstitute/SPEAQeasyWorkshop2023/SPEAQeasyWorkshop2023 - R package version 0.99.0},
#> doi = {10.18129/B9.bioc.SPEAQeasyWorkshop2023},
#> }
#>
#> 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 (2021). "SPEAQeasy: a scalable pipeline for expression
#> analysis and quantification for R/bioconductor-powered RNA-seq
#> analyses." _BMC Bioinformatics_. doi: 10.1186/s12859-021-04142-3 (URL:
#> https://doi.org/10.1186/s12859-021-04142-3), <URL:
#> https://doi.org/10.1186/s12859-021-04142-3>.
#>
#> 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 = {2021},
#> journal = {BMC Bioinformatics},
#> doi = {10.1186/s12859-021-04142-3},
#> publisher = {Springer Science and Business Media LLC},
#> url = {https://doi.org/10.1186/s12859-021-04142-3},
#> }Please note that the SPEAQeasyWorkshop2023 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 SPEAQeasyWorkshop2023 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.
