regionReport

DOI: 10.18129/B9.bioc.regionReport    

This package is for version 3.10 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: 3.10

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 "3.6") and enter:

if (!requireNamespace("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	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, ImmunoOncology, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.0 (R-3.1) (5.5 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	BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.3.2), sessioninfo, 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	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_1.20.0.tar.gz
Windows Binary	regionReport_1.20.1.zip
Mac OS X 10.11 (El Capitan)	regionReport_1.20.1.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