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README.md

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

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)

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

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

Installation instructions

Get R 3.3.x from CRAN as well as pandoc 1.17.0.3 or newer from here.

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

Vignette

The vignette for this package can be viewed 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 (2016). “regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations].” F1000Research, 4, pp. 105. doi: 10.12688/f1000research.6379.2 (URL: http://doi.org/10.12688/f1000research.6379.2), <URL: 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}, }

Testing

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