In leekgroup/regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

regionReport

Generate HTML reports for a set of regions such as those from r BiocStyle::Biocpkg('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 r BiocStyle::Biocpkg('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 r BiocStyle::Biocpkg('DESeq2') or r BiocStyle::Biocpkg('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)

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 r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), r BiocStyle::Githubpkg('r-hub/sysreqs') and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
• Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
• The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
• The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
• The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').

For more details, check the dev directory.

This package was developed using r BiocStyle::Biocpkg('biocthis').

leekgroup/regionReport documentation built on May 10, 2023, 11:37 p.m.