GitHub - leekgroup/derfinderPlot: Plotting functions for derfinder results (original) (raw)

derfinderPlot

Addon package with plotting functions forderfinder results.

Documentation

For more information about derfinderPlot check the vignettes through Bioconductor or at thedocumentation website.

Installation instructions

Get the latest stable R release fromCRAN. Then install derfinderPlot fromBioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") }

BiocManager::install("derfinderPlot")

Citation

Below is the citation output from using citation('derfinderPlot') in R. Please run this yourself to check for any updates on how to citederfinderPlot.

print(citation("derfinderPlot"), bibtex = TRUE) #> To cite package 'derfinderPlot' in publications use: #> #> Collado-Torres L, Jaffe AE, Leek JT (2017). derfinderPlot: Plotting #> functions for derfinder. doi:10.18129/B9.bioc.derfinderPlot #> https://doi.org/10.18129/B9.bioc.derfinderPlot, #> https://github.com/leekgroup/derfinderPlot - R package version #> 1.35.0, http://www.bioconductor.org/packages/derfinderPlot. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {derfinderPlot: Plotting functions for derfinder}, #> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek}, #> year = {2017}, #> url = {http://www.bioconductor.org/packages/derfinderPlot}, #> note = {https://github.com/leekgroup/derfinderPlot - R package version 1.35.0}, #> doi = {10.18129/B9.bioc.derfinderPlot}, #> } #> #> Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, #> Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible expressed region #> analysis for RNA-seq with derfinder." Nucl. Acids Res.. #> doi:10.1093/nar/gkw852 https://doi.org/10.1093/nar/gkw852, #> http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {Flexible expressed region analysis for RNA-seq with derfinder}, #> author = {Leonardo Collado-Torres and Abhinav Nellore and Alyssa C. Frazee and Christopher Wilks and Michael I. Love and Ben Langmead and Rafael A. Irizarry and Jeffrey T. Leek and Andrew E. Jaffe}, #> year = {2017}, #> journal = {Nucl. Acids Res.}, #> doi = {10.1093/nar/gkw852}, #> url = {http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852}, #> }

Please note that the derfinderPlot 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 derfinderPlot project is released with aContributor 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 actionsthrough usethis,remotes,sysreqs and_rcmdcheck_ customized to use Bioconductor’s docker containers and_BiocCheck_.
• Code coverage assessment is possible thanks tocodecov and_covr_.
• The documentation websiteis 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_.