regionReport

DOI: 10.18129/B9.bioc.regionReport    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see regionReport.

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

Bioconductor version: 3.14

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 <lcolladotor at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("regionReport")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("regionReport")

 

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, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version	1.28.1
In Bioconductor since	BioC 3.0 (R-3.1) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.2)
Imports	BiocStyle(>= 2.5.19), derfinder(>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils
LinkingTo
Suggests	BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.28.1), sessioninfo, DT, edgeR, ggbio(>= 1.35.2), 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	recountWorkflow
Suggests Me	recount
Links To Me
Build Report

Package Archives

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

Source Package	regionReport_1.28.1.tar.gz
Windows Binary	regionReport_1.28.1.zip
macOS 10.13 (High Sierra)	regionReport_1.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/regionReport
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/regionReport
Package Short Url	https://bioconductor.org/packages/regionReport/
Package Downloads Report	Download Stats