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derfinderPlot.Rmd 100644 19 kb
<!-- is generated from README.Rmd. Please edit that file --> # derfinderPlot <!-- badges: start --> [![Lifecycle: stable](]( [![Bioc release status](]( [![Bioc devel status](]( [![Bioc downloads rank](]( [![Bioc support](]( [![Bioc history](]( [![Bioc last commit](]( [![Bioc dependencies](]( [![Codecov test coverage](]( [![R build status](]( [![GitHub issues](]( [![GitHub pulls](]( <!-- badges: end --> 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: ``` r 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**. ``` r 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 #> <>, #> - R package version #> 1.35.0, <>. #> #> 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 = {}, #> note = { - 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 <>, #> <>. #> #> 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 = {}, #> } ``` 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](*.