Status: Travis CI , Bioc-release , Bioc-devel .

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)

You may also want to consult the vignette for regionReport as well as the supplementary website regionReportSupp.

Installation instructions

Get R 3.2.0 from CRAN as well as pandoc 1.12.3 or newer from here.

## From Bioconductor
source('http://bioconductor.org/biocLite.R')
biocLite('regionReport')

Vignette

The vignette for this package can be viewed here or via Bioconductor's website.

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.

To cite package regionReport in publications use:

Collado-Torres L, Jaffe AE and Leek JT (2015). regionReport: Generate HTML reports for exploring a set of regions. https://github.com/leekgroup/regionReport - R package version 1.3.4, <URL: http://www.bioconductor.org/packages/release/bioc/html/regionReport.html>.

A BibTeX entry for LaTeX users is

@Manual{, title = {regionReport: Generate HTML reports for exploring a set of regions}, author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek}, year = {2015}, url = {http://www.bioconductor.org/packages/release/bioc/html/regionReport.html}, note = {https://github.com/leekgroup/regionReport - R package version 1.3.8}, }

Testing

Testing on Bioc-devel is feasible thanks to r-builder as well as Bioconductor's nightly build.