# regionReport supplementary website

This is the supplementary website for the regionReport paper available at F1000Research.

# Example use cases

## DESeq2 case

regionReport has a specific template for DESeq2 results. The file DESEq2.html shows how to create a HTML and a PDF report using results from DESeq2. The resulting HTML report is available at DESeq2-example and the PDF version at DESeq2Report.

## edgeR case

regionReport can use edgeR results to create reports that look nearly identical to the reports from DESeq2 results along with some edgeR specific plots. The file edgeR.html shows how to create a HTML and a PDF report using results from edgeR. The resulting HTML report is available at edgeR-example and the PDF version at edgerReport. The file edgeR.html also creates a HTML report for edgeR-robust results available at edgeR-robust-example.

## bumphunter case

An example using bumphunter is showcased at bumphunterExample.html. This file shows the code for obtaining a set of simulated differentially methylated regions and creating a HTML report using renderReport(). The report is a bit simpler than the one in the example of renderReport() because there is no p-value variable. The output report from this example is available at bumphunter-example.

In case the previous links don’t work, pre-compiled versions are available. Check the following links:

## DiffBind case

An example using DiffBind is showcased at DiffBind.html. This file shows the code for obtaining a set of differentially bounded sites and creating a HTML report using renderReport() with custom code to create a MA plot and two PCA plots. This example also shows how to change the distribution plot templates to use histograms instead of density plots. The output report from this example is available at DiffBind-example and it uses rmarkdown as the engine which since version 0.9.5 allows toggling of code.

## derfinder cases

This section uses different data sets as described in the derfinder paper (bioRxiv preprint).

The reports can be viewed following these links:

Note that each report is around 40-50 MB in size and can take some time to load. These reports were generated using knitrBootstrap as the engine prior to rmarkdown v0.9.5.

The code used for generating these reports is available at the supplementary websites derSupplement and derCountSupp.

# Installation

Get R 3.2.x from CRAN as well as pandoc 1.12.3 or newer from here. Note that at the time of writing this page, some of the functionality of regionReport is only available at Bioconductor-devel (BioC version 3.3) for which you’ll need R 3.3.x.

Once you have the correct version of R, you can install regionReport directly from Bioconductor by using:

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

That command should install all the dependencies for using regionReport. This package does suggest several other packages, which you might not need to use. It will depend on the type of report that you are creating. If you wish to install them use:

## Here is the full list of suggested packages by regionReport
source('http://bioconductor.org/biocLite.R')
biocLite(c('BiocStyle', 'biovizBase', 'bumphunter', 'Cairo', 'derfinderPlot',
'devtools', 'DT', 'DESeq', 'edgeR', 'ggbio', 'ggplot2', 'grid', 'gridExtra',
'IRanges', 'mgcv', 'pasilla', 'pheatmap', 'RColorBrewer',
'TxDb.Hsapiens.UCSC.hg19.knownGene', 'whisker'))

Note that for the latest knitrBootstrap templates you will have to use:

## Install latest knitrBootstrap from GitHub
library('devtools')
install_github('jimhester/knitrBootstrap')

Some of the examples require other packages, in which case you would need to install the following packages.

## DESeq2 example
source("http://bioconductor.org/biocLite.R")
biocLite('pasilla')

## edgeR example
source("http://bioconductor.org/biocLite.R")
biocLite(c('edgeR', 'DEFormats'))

## Bumphunter example, deps are part of the suggested list of packages
source("http://bioconductor.org/biocLite.R")
biocLite(c('bumphunter', 'GenomicRanges', 'biovizBase'))

## DiffBind example
source("http://bioconductor.org/biocLite.R")
biocLite(c('DiffBind', 'biovizBase', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
'bumphunter'))

## derfinder examples. Should be installed after biocLite('regionReport')
source("http://bioconductor.org/biocLite.R")
biocLite('derfinder')

# Miscellaneous

genomicRanges.R has simple code for determining how many unique packages depend, import or suggest GenomicRanges.