README.md

In leekgroup/derfinderPlot: Plotting functions for derfinder

derfinderPlot

Addon package with plotting functions for derfinder results.

Documentation

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

Installation instructions

Get the latest stable R release from CRAN. Then install derfinderPlot from Bioconductor 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 cite derfinderPlot.

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 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, sysreqs 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.

leekgroup/derfinderPlot documentation built on May 4, 2024, 5:41 p.m.