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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # derfinderPlot <!-- badges: start --> [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/derfinderPlot.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/derfinderPlot) [![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/derfinderPlot.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/derfinderPlot) [![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/derfinderPlot.svg)](http://bioconductor.org/packages/stats/bioc/derfinderPlot/) [![Bioc support](https://bioconductor.org/shields/posts/derfinderPlot.svg)](https://support.bioconductor.org/tag/derfinderPlot) [![Bioc history](https://bioconductor.org/shields/years-in-bioc/derfinderPlot.svg)](https://bioconductor.org/packages/release/bioc/html/derfinderPlot.html#since) [![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/derfinderPlot.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinderPlot/) [![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/derfinderPlot.svg)](https://bioconductor.org/packages/release/bioc/html/derfinderPlot.html#since) [![Codecov test coverage](https://codecov.io/gh/leekgroup/derfinderPlot/branch/devel/graph/badge.svg)](https://codecov.io/gh/leekgroup/derfinderPlot?branch=devel) [![R build status](https://github.com/leekgroup/derfinderPlot/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/leekgroup/derfinderPlot/actions) [![GitHub issues](https://img.shields.io/github/issues/leekgroup/derfinderPlot)](https://github.com/leekgroup/derfinderPlot/issues) [![GitHub pulls](https://img.shields.io/github/issues-pr/leekgroup/derfinderPlot)](https://github.com/leekgroup/derfinderPlot/pulls) <!-- badges: end --> Addon package with plotting functions for [derfinder](http://www.bioconductor.org/packages/derfinder) results. ## Documentation For more information about `derfinderPlot` check the vignettes [through Bioconductor](http://bioconductor.org/packages/derfinderPlot) or at the [documentation website](http://leekgroup.github.io/derfinderPlot). ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `derfinderPlot` from [Bioconductor](http://bioconductor.org/) 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 #> <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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. ## Development tools - Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, *[sysreqs](https://github.com/r-hub/sysreqs)* and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.17/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://leekgroup.github.io/derfinderPlot) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.17/biocthis)*.