Abstract
regionReport is an R package for generating detailed interactive reports from region-level genomic analyses as well as feature-level RNA-seq. The report includes quality-control checks, an overview of the results, an interactive table of the genomic regions or features of interest and reproducibility information. regionReport provides specialised reports for exploring DESeq2, edgeR, or derfinder differential expression analyses results. regionReport is also flexible and can easily be expanded with report templates for other analysis pipelines.
Highlights
Many analyses of genomic data result in regions along the genome that associate with a covariate of interest
We considered using git2r and have not added support for so far given that (A) we mostly use regionReport in git-controlled directories that are not on the gh-pages branch and (B) that some of the reports can be large in size
We introduce regionReport which allows users to explore genomic regions of interest, derfinder, DESeq[2], and edgeR results through interactive stand-alone HTML reports that can be shared with collaborators
Summary
Made it easier to use and install dependencies via a new function load_install() based on Karthik Ram’s feedback, added a link to the bibliography file;. Modified the manuscript and added more example use cases to motivate users to use regionReport, with DESeq[2] or edgeR results which expands the software’s usefulness to a broader user base. This manuscript matches the software release from Bioconductor version 3.3 which uses by default rmarkdown’s version 0.9.5 capabilities. We might add a function for uploading the resulting report to GitHub via git2r in the future
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