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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # derfinder <!-- badges: start --> [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) [![BioC status](http://www.bioconductor.org/shields/build/release/bioc/derfinder.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/derfinder) [![BioC dev status](http://www.bioconductor.org/shields/build/devel/bioc/derfinder.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder) [![Codecov test coverage](https://codecov.io/gh/lcolladotor/derfinder/branch/master/graph/badge.svg)](https://codecov.io/gh/lcolladotor/derfinder?branch=master) [![R build status](https://github.com/lcolladotor/derfinder/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/lcolladotor/derfinder/actions) [![Support site activity, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.](http://www.bioconductor.org/shields/posts/derfinder.svg)](https://support.bioconductor.org/t/derfinder/) [![GitHub issues](https://img.shields.io/github/issues/lcolladotor/derfinder)](https://github.com/lcolladotor/derfinder/issues) <!-- badges: end --> Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. This package contains two different implementations of this approach. The first one is the single base-level F-statistics implementation and the second one is via identifying expressed regions. For more information about `derfinder` check the vignettes [here](http://www.bioconductor.org/packages/derfinder). ## Documentation For more information about `derfinder` check the vignettes [through Bioconductor](http://bioconductor.org/packages/derfinder) or at the [documentation website](http://lcolladotor.github.io/derfinder). ## Further documentation You can generate HTML reports from the results using **regionReport** available [here](https://github.com/lcolladotor/regionReport). ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `derfinder` using from [Bioconductor](http://bioconductor.org/) the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("derfinder") ``` ## Citation Below is the citation output from using `citation('derfinder')` in R. Please run this yourself to check for any updates on how to cite **derfinder**. ``` r print(citation("derfinder"), bibtex = TRUE) #> #> 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 (URL: https://doi.org/10.1093/nar/gkw852), <URL: #> 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}, #> } #> #> Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT (2014). #> "Differential expression analysis of RNA-seq data at single-base #> resolution." _Biostatistics_, *15 (3)*, 413-426. doi: #> 10.1093/biostatistics/kxt053 (URL: #> https://doi.org/10.1093/biostatistics/kxt053), <URL: #> http://biostatistics.oxfordjournals.org/content/15/3/413.long>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {Differential expression analysis of RNA-seq data at single-base resolution}, #> author = {Alyssa C. Frazee and Sarven Sabunciyan and Kasper D. Hansen and Rafael A. Irizarry and Jeffrey T. Leek}, #> year = {2014}, #> journal = {Biostatistics}, #> volume = {15 (3)}, #> pages = {413-426}, #> doi = {10.1093/biostatistics/kxt053}, #> url = {http://biostatistics.oxfordjournals.org/content/15/3/413.long}, #> } #> #> Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinder: #> Annotation-agnostic differential expression analysis of RNA-seq data at #> base-pair resolution via the DER Finder approach_. doi: #> 10.18129/B9.bioc.derfinder (URL: #> https://doi.org/10.18129/B9.bioc.derfinder), #> https://github.com/lcolladotor/derfinder - R package version 1.25.3, #> <URL: http://www.bioconductor.org/packages/derfinder>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach}, #> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek}, #> year = {2017}, #> url = {http://www.bioconductor.org/packages/derfinder}, #> note = {https://github.com/lcolladotor/derfinder - R package version 1.25.3}, #> doi = {10.18129/B9.bioc.derfinder}, #> } ``` Please note that the `derfinder` 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. ## DER Finder versions - The original implementation of the DER Finder approach as published in Frazee et al, Biostatistics 2014 is available via GitHub at [derfinder](https://github.com/leekgroup/derfinder). - The version implementing the single base-level approach via calculating F-stastics as described in the pre-print Collado-Torres et al, Nucleic Acids Research 2017 is available via Bioconductor at [derfinder](http://bioconductor.org/packages/derfinder). The same package has the functions required for the expressed regions-level approach. ## Code of Conduct Please note that the derfinder 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/3.13/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://lcolladotor.github.io/derfinder) 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/3.13/biocthis)*.