To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")

In most cases, you don't need to download the package archive at all.

regionReport

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see regionReport.

Generate HTML reports for exploring a set of regions

Bioconductor version: 3.2

Generate HTML reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder.

Author: Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>

Citation (from within R, enter citation("regionReport")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("regionReport")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("regionReport")

 

HTML Example with data from bumphunter
HTML Introduction to regionReport
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DifferentialExpression, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.4.1
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports bumphunter(>= 1.7.6), derfinder(>= 1.1.0), derfinderPlot(>= 1.3.2), devtools (>= 1.6), GenomeInfoDb, GenomicRanges, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), mgcv, RColorBrewer, rmarkdown (>= 0.3.3), whisker
LinkingTo
Suggests BiocStyle, biovizBase, Cairo, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL https://github.com/leekgroup/regionReport
BugReports https://github.com/leekgroup/regionReport/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source regionReport_1.4.1.tar.gz
Windows Binary regionReport_1.4.1.zip
Mac OS X 10.6 (Snow Leopard) regionReport_1.4.1.tgz
Mac OS X 10.9 (Mavericks) regionReport_1.4.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/regionReport/tree/release-3.2
Package Short Url http://bioconductor.org/packages/regionReport/
Package Downloads Report Download Stats

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