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

DOI: 10.18129/B9.bioc.regionReport    

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

Bioconductor version: Release (3.6)

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 1.12.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports BiocStyle(>= 2.5.19), 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 biovizBase, bumphunter(>= 1.7.6), 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://support.bioconductor.org/t/regionReport/
Depends On Me
Imports Me
Suggests Me recount
Build Report  

Package Archives

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

Source Package regionReport_1.12.0.tar.gz
Windows Binary regionReport_1.12.0.zip
Mac OS X 10.11 (El Capitan) regionReport_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/regionReport
Package Short Url http://bioconductor.org/packages/regionReport/
Package Downloads Report Download Stats

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