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

 

   

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Bioconductor version: Release (3.4)

Generate HTML or PDF 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. You can also create reports for DESeq2 or edgeR results.

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

HTML R Script Basic genomic regions exploration
HTML R Script Example report using bumphunter results
HTML R Script Introduction to regionReport
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version 1.8.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports derfinder(>= 1.1.0), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment
LinkingTo
Suggests BiocStyle, biovizBase, bumphunter(>= 1.7.6), Cairo, derfinderPlot(>= 1.3.2), devtools (>= 1.6), DT, DESeq, edgeR, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
SystemRequirements
Enhances
URL https://github.com/leekgroup/regionReport
BugReports https://github.com/leekgroup/regionReport/issues
Depends On Me
Imports Me
Suggests Me recount
Build Report  

Package Archives

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

Package Source regionReport_1.8.0.tar.gz
Windows Binary regionReport_1.8.0.zip
Mac OS X 10.9 (Mavericks) regionReport_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/regionReport/tree/release-3.4
Package Short Url http://bioconductor.org/packages/regionReport/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: