README.md

regionReport

Generate HTML reports for a set of regions such as those from derfinder results or any other pipeline that defines a set of genomic regions.

Check the documentation for derfinderReport() for an example on how to create the necessary input files and generating the HTML report for derfinder results. Or use:

example("derfinderReport", "regionReport", ask = FALSE)

Similarly, check renderReport() for an example of a general report, or use:

example("renderReport", "regionReport", ask = FALSE)

For DESeq2 or edgeR results check DESeq2Report() and edgeReport().

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 regionReport from Bioconductor using the following code:

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

BiocManager::install("regionReport")

Citation

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

print(citation("regionReport"), bibtex = TRUE)
#> To cite package 'regionReport' in publications use:
#> 
#>   Collado-Torres L, Jaffe AE, Leek JT (2016). "regionReport:
#>   Interactive reports for region-level and feature-level genomic
#>   analyses [version2; referees: 2 approved, 1 approved with
#>   reservations]." _F1000Research_, *4*, 105.
#>   doi:10.12688/f1000research.6379.2
#>   <https://doi.org/10.12688/f1000research.6379.2>,
#>   <http://f1000research.com/articles/4-105/v2>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#>     title = {regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]},
#>     journal = {F1000Research},
#>     year = {2016},
#>     doi = {10.12688/f1000research.6379.2},
#>     url = {http://f1000research.com/articles/4-105/v2},
#>     volume = {4},
#>     pages = {105},
#>   }
#> 
#>   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},
#>   }
#> 
#>   Collado-Torres L, Jaffe AE, Leek JT (2017). _regionReport: Generate
#>   HTML or PDF reports for a set of genomic regions or DESeq2/edgeR
#>   results_. doi:10.18129/B9.bioc.regionReport
#>   <https://doi.org/10.18129/B9.bioc.regionReport>,
#>   https://github.com/leekgroup/regionReport - R package version 1.35.0,
#>   <http://www.bioconductor.org/packages/regionReport>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results},
#>     author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#>     year = {2017},
#>     url = {http://www.bioconductor.org/packages/regionReport},
#>     note = {https://github.com/leekgroup/regionReport - R package version 1.35.0},
#>     doi = {10.18129/B9.bioc.regionReport},
#>   }

Please note that the regionReport 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 regionReport 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.